
#######################################################
#                                                     #
#                        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:    16      18_A - 33_A        4.47    19.15
  LCS_AVERAGE:     43.53

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      15_A - 23_A        1.98    18.23
  LCS_AVERAGE:     24.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.79    26.73
  LCS_AVERAGE:     15.61

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      6    8   12      3    4    7    7    7    8    8    9    9    9    9    9    9   12   12   12   13   14   14   14 
LCS_GDT     R     2_A     R     2_A      6    8   12      4    4    7    7    7    8    8    9    9    9    9    9   11   12   12   12   13   14   14   14 
LCS_GDT     Q     3_A     Q     3_A      6    8   12      4    4    7    7    7    8    8    9    9    9    9   10   11   12   12   12   13   14   14   14 
LCS_GDT     S     4_A     S     4_A      6    8   12      4    4    7    7    7    8    8    9    9    9    9   11   11   12   12   12   13   14   14   14 
LCS_GDT     S     5_A     S     5_A      6    8   12      4    4    7    7    7    8    8    9   10   10   11   11   12   12   12   13   13   14   14   14 
LCS_GDT     A     6_A     A     6_A      6    8   12      3    4    7    7    7    8    8    9   10   10   11   11   12   12   12   13   13   14   14   14 
LCS_GDT     T     7_A     T     7_A      5    8   12      3    4    7    7    7    8    8    9   10   10   11   11   12   12   12   13   13   14   14   15 
LCS_GDT     S     8_A     S     8_A      3    8   12      3    3    4    5    7    8    8    9   10   10   11   11   12   12   12   13   13   14   16   19 
LCS_GDT     S     9_A     S     9_A      3    5   12      3    3    3    4    5    8    8    9   10   10   11   11   12   12   12   13   13   14   14   14 
LCS_GDT     F    10_A     F    10_A      3    7   12      3    3    3    4    6    8    8    9   10   10   11   11   12   12   12   13   13   14   14   15 
LCS_GDT     G    11_A     G    11_A      3    7   14      3    3    3    4    6    8    8    9   10   10   11   11   13   13   15   17   17   18   18   20 
LCS_GDT     G    12_A     G    12_A      3    7   14      3    3    4    4    6    8    8    9   10   10   11   12   13   14   15   17   17   18   19   21 
LCS_GDT     L    13_A     L    13_A      4    7   14      3    4    4    4    5    8    9   10   10   10   11   12   13   14   14   16   17   18   19   21 
LCS_GDT     G    14_A     G    14_A      4    7   14      3    4    5    6    8    9    9   10   12   12   12   12   13   14   14   14   15   17   18   21 
LCS_GDT     G    15_A     G    15_A      4    9   14      3    4    4    6    8    9    9   11   12   12   12   12   13   14   14   14   15   16   18   21 
LCS_GDT     G    16_A     G    16_A      4    9   14      0    4    5    6    8    9    9   11   12   12   12   12   13   14   14   14   15   17   19   21 
LCS_GDT     S    17_A     S    17_A      5    9   14      3    5    5    5    8    9    9   11   12   12   12   12   13   14   14   14   15   17   19   21 
LCS_GDT     V    18_A     V    18_A      5    9   16      3    5    5    6    8    9    9   11   12   12   12   14   15   15   15   17   17   18   19   21 
LCS_GDT     R    19_A     R    19_A      5    9   16      3    5    5    5    8    9    9   11   12   12   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     F    20_A     F    20_A      5    9   16      4    5    5    6    8    9    9   11   12   12   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     G    21_A     G    21_A      5    9   16      4    5    5    6    8    9   10   11   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     P    22_A     P    22_A      5    9   16      4    4    5    6    8    9   10   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     G    23_A     G    23_A      5    9   16      4    4    5    6    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     V    24_A     V    24_A      5    7   16      3    4    5    6    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     A    25_A     A    25_A      5    7   16      3    4    5    6    6    7   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     F    26_A     F    26_A      7    8   16      3    6    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     R    27_A     R    27_A      7    8   16      3    6    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     A    28_A     A    28_A      7    8   16      4    6    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     P    29_A     P    29_A      7    8   16      4    6    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     S    30_A     S    30_A      7    8   16      4    6    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     I    31_A     I    31_A      7    8   16      4    6    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     H    32_A     H    32_A      7    8   16      3    5    7    7    8    9   11   12   12   13   14   14   15   15   15   17   17   18   19   21 
LCS_GDT     G    33_A     G    33_A      4    8   16      3    4    4    5    8    9   11   12   12   13   13   13   14   15   15   16   17   18   18   19 
LCS_AVERAGE  LCS_A:  27.76  (  15.61   24.15   43.53 )

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      7      7      8      9     11     12     12     13     14     14     15     15     15     17     17     18     19     21 
GDT PERCENT_AT  12.12  18.18  21.21  21.21  24.24  27.27  33.33  36.36  36.36  39.39  42.42  42.42  45.45  45.45  45.45  51.52  51.52  54.55  57.58  63.64
GDT RMS_LOCAL    0.14   0.65   0.79   0.79   1.34   1.92   2.58   2.76   2.76   3.03   3.73   3.73   4.24   3.95   3.95   5.38   5.04   5.51   6.52   7.10
GDT RMS_ALL_AT  25.81  27.59  26.73  26.73  26.87  17.57  20.16  20.00  20.00  19.76  19.68  19.68  19.05  19.65  19.65  18.08  18.60  18.24  17.35  17.15

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  F    26_A      F    26_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    49.975     0    0.618   1.531    53.548    0.000    0.000
LGA    R     2_A      R     2_A    43.907     0    0.025   0.935    46.068    0.000    0.000
LGA    Q     3_A      Q     3_A    40.654     0    0.012   0.642    44.977    0.000    0.000
LGA    S     4_A      S     4_A    35.347     0    0.012   0.021    37.127    0.000    0.000
LGA    S     5_A      S     5_A    32.451     0    0.277   0.335    34.579    0.000    0.000
LGA    A     6_A      A     6_A    29.216     0    0.401   0.449    30.816    0.000    0.000
LGA    T     7_A      T     7_A    22.357     0    0.673   0.562    24.739    0.000    0.000
LGA    S     8_A      S     8_A    16.612     0    0.628   0.833    18.854    0.000    0.000
LGA    S     9_A      S     9_A    17.911     0    0.662   0.753    19.352    0.000    0.000
LGA    F    10_A      F    10_A    15.566     0    0.223   1.116    17.362    0.000    0.000
LGA    G    11_A      G    11_A    10.096     0    0.645   0.645    12.721    0.000    0.000
LGA    G    12_A      G    12_A    13.958     0    0.155   0.155    14.261    0.000    0.000
LGA    L    13_A      L    13_A    16.983     0    0.027   0.071    20.638    0.000    0.000
LGA    G    14_A      G    14_A    21.557     0    0.144   0.144    23.115    0.000    0.000
LGA    G    15_A      G    15_A    21.200     0    0.642   0.642    21.200    0.000    0.000
LGA    G    16_A      G    16_A    18.591     0    0.556   0.556    19.986    0.000    0.000
LGA    S    17_A      S    17_A    17.873     0    0.215   0.662    19.842    0.000    0.000
LGA    V    18_A      V    18_A    12.262     0    0.155   1.104    14.648    0.000    0.000
LGA    R    19_A      R    19_A    10.084     0    0.365   0.969    18.027    2.143    0.909
LGA    F    20_A      F    20_A     9.314     0    0.023   1.228    16.159    1.786    0.649
LGA    G    21_A      G    21_A     5.779     0    0.049   0.049     6.614   24.405   24.405
LGA    P    22_A      P    22_A     3.522     0    0.466   0.670     5.318   38.810   36.599
LGA    G    23_A      G    23_A     3.627     0    0.277   0.277     3.627   55.833   55.833
LGA    V    24_A      V    24_A     1.651     0    0.033   0.059     5.644   81.548   60.340
LGA    A    25_A      A    25_A     3.733     0    0.164   0.175     6.640   42.381   36.571
LGA    F    26_A      F    26_A     3.646     0    0.413   1.173     8.532   61.429   29.654
LGA    R    27_A      R    27_A     2.121     0    0.115   1.242    12.811   61.190   30.043
LGA    A    28_A      A    28_A     2.201     0    0.024   0.022     3.833   81.786   74.095
LGA    P    29_A      P    29_A     2.563     0    0.040   0.337     6.095   69.405   51.905
LGA    S    30_A      S    30_A     1.728     0    0.033   0.045     4.247   79.405   66.349
LGA    I    31_A      I    31_A     2.030     0    0.287   1.306     5.489   63.095   50.536
LGA    H    32_A      H    32_A     1.885     0    0.005   1.177     9.086   72.976   39.571
LGA    G    33_A      G    33_A     3.077     0    0.024   0.024     5.995   43.929   43.929

# 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):    15.155         14.967                 16.768           23.640   18.224

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     12    2.76    31.818    30.174     0.419

LGA_LOCAL      RMSD:   2.762  Number of atoms:   12  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.001  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  15.155  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.371513 * X  +   0.813433 * Y  +  -0.447553 * Z  + -37.129974
  Y_new =   0.618349 * X  +   0.142795 * Y  +   0.772822 * Z  + -18.856880
  Z_new =   0.692547 * X  +  -0.563858 * Y  +  -0.449936 * Z  +  22.901306 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.029778 -0.765014 -2.244292   [DEG:   59.0019  -43.8321 -128.5885 ]
ZXZ: -2.616671  2.037490  2.254124   [DEG: -149.9242  116.7396  129.1518 ]
 
# END of job
