
#######################################################
#                                                     #
#                        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:    23      13_A - 35_A        4.97     8.16
  LCS_AVERAGE:     58.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      23_A - 29_A        1.40     8.84
  LCS_AVERAGE:     14.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       7_A - 11_A        0.48    17.73
  LONGEST_CONTINUOUS_SEGMENT:     5      16_A - 20_A        0.58    15.65
  LCS_AVERAGE:     10.86

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    3   12      3    3    3    3    7    8   10   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     D     2_A     D     2_A      3    3   12      3    3    3    3    3    3    4   11   15   18   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     E     3_A     E     3_A      3    3   12      3    3    3    3    3    3    5    7    9    9   10   15   23   24   26   27   29   30   31   33 
LCS_GDT     M     4_A     M     4_A      3    3   12      3    3    4    5    5    5    5    8    9   13   16   20   23   24   26   27   29   30   31   33 
LCS_GDT     W     5_A     W     5_A      3    3   12      1    3    4    5    5    5    5    7    9    9   13   16   21   23   26   27   29   30   31   33 
LCS_GDT     F     6_A     F     6_A      3    3   18      3    3    4    5    5    5    5    7    9    9   12   16   21   22   25   27   29   30   31   33 
LCS_GDT     C     7_A     C     7_A      5    5   18      4    5    5    5    5    5    5    7    9   10   12   15   18   22   25   26   29   30   31   33 
LCS_GDT     E     8_A     E     8_A      5    5   18      4    5    5    5    5    5    8    9   11   13   15   16   17   19   21   24   26   27   29   30 
LCS_GDT     T     9_A     T     9_A      5    5   18      4    5    5    5    5    5    5    7    9   12   15   16   17   17   17   18   20   23   24   27 
LCS_GDT     L    10_A     L    10_A      5    5   18      4    5    5    5    5    5    6    7    9   12   15   16   18   21   25   26   29   30   31   33 
LCS_GDT     R    11_A     R    11_A      5    5   18      4    5    5    5    5    5    8    9   11   13   15   17   21   23   26   27   29   30   31   33 
LCS_GDT     R    12_A     R    12_A      3    4   22      3    3    4    5    6    8   10   13   15   16   19   20   23   24   26   27   29   30   31   33 
LCS_GDT     L    13_A     L    13_A      3    4   23      3    3    5    6    7    9   10   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     L    14_A     L    14_A      4    4   23      3    4    4    6    6    7   11   13   15   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     C    15_A     C    15_A      4    6   23      3    4    4    6    8   10   11   13   15   16   18   21   21   23   25   26   27   28   31   33 
LCS_GDT     P    16_A     P    16_A      5    6   23      3    5    5    6    7   10   10   12   15   15   16   18   19   21   25   25   27   28   29   33 
LCS_GDT     K    17_A     K    17_A      5    6   23      3    5    5    6    8   10   11   13   15   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     S    18_A     S    18_A      5    6   23      3    5    5    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     C    19_A     C    19_A      5    6   23      3    5    5    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     S    20_A     S    20_A      5    6   23      3    5    5    6    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     I    21_A     I    21_A      4    6   23      3    3    4    5    6   10   10   12   15   15   16   19   23   24   26   27   29   30   31   33 
LCS_GDT     E    22_A     E    22_A      4    6   23      3    3    5    6    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     G    23_A     G    23_A      4    7   23      3    6    6    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     G    24_A     G    24_A      4    7   23      3    6    6    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     C    25_A     C    25_A      4    7   23      3    6    6    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     P    26_A     P    26_A      4    7   23      3    4    4    6    7    9   10   13   15   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     E    27_A     E    27_A      3    7   23      3    6    6    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     V    28_A     V    28_A      3    7   23      3    6    6    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     C    29_A     C    29_A      3    7   23      3    6    6    8    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     S    30_A     S    30_A      3    4   23      3    4    5    6    7    9   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     H    31_A     H    31_A      3    4   23      3    3    3    5    5    7   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     M    32_A     M    32_A      3    4   23      3    3    4    5    8   10   11   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     C    33_A     C    33_A      3    4   23      3    3    3    5    5    8   10   13   16   19   20   21   23   24   26   27   29   30   31   33 
LCS_GDT     P    34_A     P    34_A      3    4   23      3    3    3    3    4    8   10   10   11   11   13   19   20   23   25   26   27   28   29   33 
LCS_GDT     L    35_A     L    35_A      3    4   23      0    3    4    5    5    5    7    9   14   14   17   19   20   23   25   26   27   30   31   33 
LCS_AVERAGE  LCS_A:  27.97  (  10.86   14.37   58.69 )

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      6      6      8      8     10     11     13     16     19     20     21     23     24     26     27     29     30     31     33 
GDT PERCENT_AT  11.43  17.14  17.14  22.86  22.86  28.57  31.43  37.14  45.71  54.29  57.14  60.00  65.71  68.57  74.29  77.14  82.86  85.71  88.57  94.29
GDT RMS_LOCAL    0.15   0.77   0.77   1.37   1.37   2.02   2.22   2.63   3.39   3.79   3.88   4.04   4.49   4.61   5.05   5.29   5.74   5.94   6.08   6.44
GDT RMS_ALL_AT  17.80   9.31   9.31  10.78  10.78  11.76  11.81  10.21   7.73   7.76   7.68   7.81   7.34   7.35   7.20   7.16   7.10   7.03   7.04   7.07

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E     3_A      E     3_A
#   possible swapping detected:  E     8_A      E     8_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    14.396     0    0.120   0.165    15.798    0.000    0.000
LGA    D     2_A      D     2_A    12.361     0    0.597   1.217    14.058    0.000    0.000
LGA    E     3_A      E     3_A    11.469     0    0.569   0.782    11.866    0.000    0.000
LGA    M     4_A      M     4_A    13.372     0    0.620   0.945    20.207    0.000    0.000
LGA    W     5_A      W     5_A    13.451     0    0.570   1.138    15.308    0.000    0.000
LGA    F     6_A      F     6_A    15.887     0    0.600   0.642    19.715    0.000    0.000
LGA    C     7_A      C     7_A    15.567     0    0.590   0.523    16.496    0.000    0.000
LGA    E     8_A      E     8_A    17.255     0    0.094   0.932    20.660    0.000    0.000
LGA    T     9_A      T     9_A    21.103     0    0.030   0.187    24.202    0.000    0.000
LGA    L    10_A      L    10_A    18.325     0    0.189   0.175    21.939    0.000    0.000
LGA    R    11_A      R    11_A    14.880     0    0.441   0.530    21.821    0.000    0.000
LGA    R    12_A      R    12_A    13.571     0    0.657   0.948    19.478    0.000    0.000
LGA    L    13_A      L    13_A     9.377     0    0.619   1.034    12.335    5.357    2.738
LGA    L    14_A      L    14_A     4.971     0    0.661   0.539    11.618   45.595   24.524
LGA    C    15_A      C    15_A     2.147     0    0.021   0.887     6.574   68.810   53.333
LGA    P    16_A      P    16_A     5.378     0    0.603   0.753     8.542   37.500   24.966
LGA    K    17_A      K    17_A     1.524     0    0.044   0.711     2.974   80.119   81.905
LGA    S    18_A      S    18_A     2.569     0    0.050   0.098     3.449   57.262   54.841
LGA    C    19_A      C    19_A     2.101     0    0.494   0.537     2.502   64.881   64.841
LGA    S    20_A      S    20_A     2.894     0    0.675   0.831     5.841   45.119   43.651
LGA    I    21_A      I    21_A     5.645     0    0.067   0.343    11.733   32.024   17.917
LGA    E    22_A      E    22_A     0.483     0    0.031   0.959     6.275   70.238   50.635
LGA    G    23_A      G    23_A     3.347     0    0.679   0.679     3.347   67.143   67.143
LGA    G    24_A      G    24_A     1.705     0    0.076   0.076     3.509   63.452   63.452
LGA    C    25_A      C    25_A     3.654     0    0.316   0.798     5.309   38.214   44.524
LGA    P    26_A      P    26_A     9.617     0    0.698   0.628    12.035    2.024    1.361
LGA    E    27_A      E    27_A     8.499     0    0.071   0.940     9.514    4.286    3.280
LGA    V    28_A      V    28_A     8.282     0    0.555   0.816    11.514    9.048    5.306
LGA    C    29_A      C    29_A     4.072     0    0.617   0.971     5.682   41.429   42.063
LGA    S    30_A      S    30_A     1.563     0    0.601   0.863     3.555   67.619   61.746
LGA    H    31_A      H    31_A     3.327     0    0.468   1.370    11.066   67.262   30.524
LGA    M    32_A      M    32_A     2.343     0    0.594   1.224     7.336   59.405   45.714
LGA    C    33_A      C    33_A     5.679     0    0.301   0.338     9.482   16.786   16.984
LGA    P    34_A      P    34_A    10.772     0    0.504   0.436    11.397    1.190    2.177
LGA    L    35_A      L    35_A    13.187     0    0.364   0.551    17.149    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):     7.011          6.827                  8.327           26.993   22.961

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     13    2.63    38.571    32.815     0.477

LGA_LOCAL      RMSD:   2.625  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.211  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   7.011  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.272472 * X  +  -0.487701 * Y  +  -0.829401 * Z  +  -6.959805
  Y_new =   0.945439 * X  +  -0.024316 * Y  +   0.324890 * Z  +  -3.342692
  Z_new =  -0.178617 * X  +  -0.872672 * Y  +   0.454467 * Z  +   4.926388 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.290204  0.179581 -1.090666   [DEG:   73.9232   10.2892  -62.4906 ]
ZXZ: -1.944141  1.099023 -2.939703   [DEG: -111.3911   62.9694 -168.4326 ]
 
# END of job
