
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , 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:    20       6_A - 25_A        4.53    15.05
  LONGEST_CONTINUOUS_SEGMENT:    20       7_A - 26_A        4.80    14.53
  LONGEST_CONTINUOUS_SEGMENT:    20      14_A - 33_A        4.65    11.33
  LCS_AVERAGE:     58.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       9_A - 21_A        1.99    15.36
  LCS_AVERAGE:     29.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      25_A - 31_A        0.99    14.69
  LCS_AVERAGE:     13.96

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      3    4   14      0    3    3    4    5    5    6    6   13   14   16   16   18   18   19   21   21   21   22   23 
LCS_GDT     R     2_A     R     2_A      3    4   14      0    3    3    4    5    5    6   11   13   14   16   16   18   18   19   21   21   21   22   23 
LCS_GDT     Q     3_A     Q     3_A      3    4   14      0    3    3    5    5   10   11   12   13   14   16   16   18   18   19   21   21   21   22   23 
LCS_GDT     S     4_A     S     4_A      3    4   15      0    3    4    5    7   10   11   12   13   14   16   16   18   18   19   21   21   21   22   23 
LCS_GDT     S     5_A     S     5_A      3    4   17      3    3    4    5    5   10   11   12   13   14   16   16   18   18   19   21   21   21   22   23 
LCS_GDT     A     6_A     A     6_A      3    4   20      3    3    4    4    4    7    8   12   13   15   16   17   18   19   19   21   21   21   22   23 
LCS_GDT     T     7_A     T     7_A      3    4   20      3    3    4    4    5    7   10   11   14   16   17   17   18   19   19   20   20   21   21   22 
LCS_GDT     S     8_A     S     8_A      3    4   20      3    3    3    4    5    9   10   12   15   16   17   17   18   19   19   19   20   21   21   21 
LCS_GDT     S     9_A     S     9_A      4   13   20      3    4    7    8   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     F    10_A     F    10_A      4   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     G    11_A     G    11_A      4   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     G    12_A     G    12_A      4   13   20      3    4    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     L    13_A     L    13_A      4   13   20      3    3    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     G    14_A     G    14_A      5   13   20      3    4    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     G    15_A     G    15_A      5   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     G    16_A     G    16_A      5   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     S    17_A     S    17_A      5   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     V    18_A     V    18_A      5   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   19   20   21   23   23 
LCS_GDT     R    19_A     R    19_A      5   13   20      1    5    6    8   10   12   14   14   15   16   17   17   18   19   19   21   21   21   22   23 
LCS_GDT     F    20_A     F    20_A      4   13   20      1    5    6    9   11   12   14   14   15   16   17   17   18   19   19   21   21   21   23   23 
LCS_GDT     G    21_A     G    21_A      4   13   20      3    5    7    9   11   12   14   14   15   16   17   17   18   19   19   21   21   21   23   23 
LCS_GDT     P    22_A     P    22_A      4    8   20      3    3    4    6    7   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     G    23_A     G    23_A      4   10   20      3    4    7    8   11   12   14   14   15   16   17   17   18   19   19   21   21   21   23   23 
LCS_GDT     V    24_A     V    24_A      4   10   20      3    6    6    8   10   11   13   14   15   16   17   17   18   19   19   21   21   21   23   23 
LCS_GDT     A    25_A     A    25_A      7   10   20      4    6    8    8    9   10   13   14   15   16   16   17   18   19   19   21   21   21   23   23 
LCS_GDT     F    26_A     F    26_A      7   10   20      4    5    8    8    9   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     R    27_A     R    27_A      7   10   20      4    5    8    8    9   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     A    28_A     A    28_A      7   10   20      3    6    8    8    9   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     P    29_A     P    29_A      7   10   20      4    6    8    8    9   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     S    30_A     S    30_A      7   10   20      4    6    8    8    9   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     I    31_A     I    31_A      7   10   20      4    6    8    8    9   10   12   14   15   15   16   17   18   18   19   21   21   21   22   23 
LCS_GDT     H    32_A     H    32_A      6   10   20      4    6    8    8    9   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_GDT     G    33_A     G    33_A      3   10   20      4    5    6    7    7   10   13   14   15   16   16   17   18   18   19   21   21   21   23   23 
LCS_AVERAGE  LCS_A:  33.82  (  13.96   29.29   58.22 )

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      8      9     11     12     14     14     15     16     17     17     18     19     19     21     21     21     23     23 
GDT PERCENT_AT  12.12  18.18  24.24  27.27  33.33  36.36  42.42  42.42  45.45  48.48  51.52  51.52  54.55  57.58  57.58  63.64  63.64  63.64  69.70  69.70
GDT RMS_LOCAL    0.21   0.67   1.01   1.31   1.57   1.73   2.17   2.17   2.42   3.03   3.39   3.39   3.70   4.20   4.12   5.34   5.34   5.02   6.52   6.42
GDT RMS_ALL_AT  11.61  15.61  14.67  14.77  15.01  15.31  15.14  15.14  15.25  15.01  15.10  15.10  12.23  14.87  11.82  13.73  13.73  13.71   9.67  13.00

# Checking swapping
#   possible swapping detected:  F    10_A      F    10_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    24.658     0    0.295   1.172    29.345    0.000    0.000
LGA    R     2_A      R     2_A    23.140     0    0.618   1.264    30.843    0.000    0.000
LGA    Q     3_A      Q     3_A    21.037     0    0.527   1.421    22.354    0.000    0.000
LGA    S     4_A      S     4_A    20.154     0    0.555   0.713    21.395    0.000    0.000
LGA    S     5_A      S     5_A    17.450     0    0.400   0.529    17.963    0.000    0.000
LGA    A     6_A      A     6_A    12.713     0    0.040   0.055    14.140    0.000    0.000
LGA    T     7_A      T     7_A    10.216     0    0.080   1.034    11.109    1.071    0.884
LGA    S     8_A      S     8_A     7.849     0    0.562   0.733    10.768   16.548   11.111
LGA    S     9_A      S     9_A     2.606     0    0.626   0.760     5.691   52.262   43.651
LGA    F    10_A      F    10_A     0.872     0    0.676   1.090     8.245   75.833   48.485
LGA    G    11_A      G    11_A     0.905     0    0.657   0.657     2.118   79.524   79.524
LGA    G    12_A      G    12_A     2.690     0    0.428   0.428     4.205   54.048   54.048
LGA    L    13_A      L    13_A     1.273     0    0.434   0.399     4.276   79.524   63.393
LGA    G    14_A      G    14_A     1.651     0    0.406   0.406     3.052   65.119   65.119
LGA    G    15_A      G    15_A     2.600     0    0.630   0.630     3.380   63.690   63.690
LGA    G    16_A      G    16_A     2.478     0    0.606   0.606     4.539   54.524   54.524
LGA    S    17_A      S    17_A     0.560     0    0.183   0.177     1.838   88.452   86.111
LGA    V    18_A      V    18_A     0.821     0    0.117   1.149     2.624   82.024   77.211
LGA    R    19_A      R    19_A     3.430     0    0.582   1.090     5.713   52.262   38.745
LGA    F    20_A      F    20_A     1.948     0    0.362   1.241     9.019   57.262   32.208
LGA    G    21_A      G    21_A     2.731     0    0.268   0.268     2.920   60.952   60.952
LGA    P    22_A      P    22_A     5.143     0    0.070   0.101     7.468   30.476   23.741
LGA    G    23_A      G    23_A     3.035     0    0.601   0.601     5.950   43.929   43.929
LGA    V    24_A      V    24_A     6.971     0    0.232   0.300     8.868   13.095   11.701
LGA    A    25_A      A    25_A    11.845     0    0.248   0.272    14.297    0.000    0.000
LGA    F    26_A      F    26_A    13.258     0    0.027   0.343    17.136    0.000    0.000
LGA    R    27_A      R    27_A    18.667     0    0.030   0.914    29.385    0.000    0.000
LGA    A    28_A      A    28_A    19.455     0    0.155   0.188    22.267    0.000    0.000
LGA    P    29_A      P    29_A    19.910     0    0.077   0.421    23.339    0.000    0.000
LGA    S    30_A      S    30_A    26.144     0    0.447   0.517    27.647    0.000    0.000
LGA    I    31_A      I    31_A    29.411     0    0.614   1.524    34.978    0.000    0.000
LGA    H    32_A      H    32_A    29.979     0    0.617   1.022    30.018    0.000    0.000
LGA    G    33_A      G    33_A    30.226     0    0.472   0.472    30.870    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):     9.057          9.008                 10.123           29.412   26.031

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.17    37.879    36.988     0.616

LGA_LOCAL      RMSD:   2.172  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.142  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.057  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.839639 * X  +  -0.150651 * Y  +  -0.521834 * Z  +  44.801254
  Y_new =   0.503955 * X  +  -0.574413 * Y  +  -0.645042 * Z  +  15.847096
  Z_new =  -0.202572 * X  +  -0.804583 * Y  +   0.558221 * Z  +  21.851646 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.601023  0.203984 -0.964243   [DEG:  149.0276   11.6874  -55.2470 ]
ZXZ: -0.680200  0.978556 -2.894946   [DEG:  -38.9726   56.0671 -165.8682 ]
 
# END of job
