
#######################################################
#                                                     #
#                        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   42 (  352),  selected   42 , name one
# Molecule2: number of CA atoms   97 (  780),  selected   42 , 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:    29       5_A - 33_A        4.08    29.49
  LCS_AVERAGE:     26.71

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26       5_A - 30_A        1.63    29.95
  LCS_AVERAGE:     23.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       5_A - 27_A        0.91    29.78
  LONGEST_CONTINUOUS_SEGMENT:    23       6_A - 28_A        0.93    29.89
  LCS_AVERAGE:     18.88

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   42
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     I     5_A     I     5_A     23   26   29      1    3    9   21   22   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     K     6_A     K     6_A     23   26   29      0    3    4   10   15   24   24   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     G     7_A     G     7_A     23   26   29     14   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     Y     8_A     Y     8_A     23   26   29     17   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     E     9_A     E     9_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     Y    10_A     Y    10_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     Q    11_A     Q    11_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     L    12_A     L    12_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     Y    13_A     Y    13_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     V    14_A     V    14_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     Y    15_A     Y    15_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     A    16_A     A    16_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     S    17_A     S    17_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     D    18_A     D    18_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     K    19_A     K    19_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     L    20_A     L    20_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     F    21_A     F    21_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     R    22_A     R    22_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     A    23_A     A    23_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     D    24_A     D    24_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     I    25_A     I    25_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     S    26_A     S    26_A     23   26   29     18   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     E    27_A     E    27_A     23   26   29     14   21   21   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     D    28_A     D    28_A     23   26   29      4   10   20   22   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     Y    29_A     Y    29_A      5   26   29      4    6   15   21   23   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     K    30_A     K    30_A      5   26   29      4    5   11   15   22   25   25   26   26   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     T    31_A     T    31_A      4   17   29      3    3   10   13   16   18   18   18   21   26   27   27   27   27   28   28   28   28   28   29 
LCS_GDT     R    32_A     R    32_A      7   17   29      3    4    7    7   12   18   18   18   19   20   20   20   20   22   28   28   28   28   28   29 
LCS_GDT     G    33_A     G    33_A     14   17   29     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   27   29 
LCS_GDT     R    34_A     R    34_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     K    35_A     K    35_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     L    36_A     L    36_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     L    37_A     L    37_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     R    38_A     R    38_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     F    39_A     F    39_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     N    40_A     N    40_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     G    41_A     G    41_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     P    42_A     P    42_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     V    43_A     V    43_A     14   17   19      3   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     P    44_A     P    44_A     14   17   19      3   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     P    45_A     P    45_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_GDT     P    46_A     P    46_A     14   17   19     10   14   14   15   16   18   18   18   19   20   20   20   20   22   22   22   22   22   22   22 
LCS_AVERAGE  LCS_A:  22.95  (  18.88   23.27   26.71 )

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     18     21     21     22     23     25     25     26     26     26     27     27     27     27     28     28     28     28     28     29 
GDT PERCENT_AT  18.56  21.65  21.65  22.68  23.71  25.77  25.77  26.80  26.80  26.80  27.84  27.84  27.84  27.84  28.87  28.87  28.87  28.87  28.87  29.90
GDT RMS_LOCAL    0.22   0.39   0.39   0.67   1.00   1.45   1.45   1.63   1.63   1.63   2.24   2.24   2.24   2.24   3.05   3.05   3.05   3.05   3.05   4.08
GDT RMS_ALL_AT  29.79  29.82  29.82  29.89  29.92  29.94  29.94  29.95  29.95  29.95  29.90  29.90  29.90  29.90  29.75  29.75  29.75  29.75  29.75  29.49

# Checking swapping
#   possible swapping detected:  Y     8_A      Y     8_A
#   possible swapping detected:  Y    10_A      Y    10_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  F    21_A      F    21_A
#   possible swapping detected:  D    24_A      D    24_A
#   possible swapping detected:  F    39_A      F    39_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I     5_A      I     5_A     2.567     0    0.108   0.133     6.810   66.905   50.060
LGA    K     6_A      K     6_A     3.885     0    0.648   1.280    13.752   45.119   23.016
LGA    G     7_A      G     7_A     0.744     0    0.161   0.161     1.227   88.214   88.214
LGA    Y     8_A      Y     8_A     0.397     0    0.011   0.236     3.551  100.000   77.024
LGA    E     9_A      E     9_A     0.606     0    0.082   0.773     4.127   90.595   75.185
LGA    Y    10_A      Y    10_A     0.321     0    0.040   0.088     1.442   92.857   88.254
LGA    Q    11_A      Q    11_A     0.632     0    0.015   1.154     5.790   92.857   72.857
LGA    L    12_A      L    12_A     0.546     0    0.020   0.502     1.684   92.857   88.333
LGA    Y    13_A      Y    13_A     0.901     0    0.034   0.119     1.571   90.476   83.730
LGA    V    14_A      V    14_A     0.698     0    0.013   1.187     2.571   90.476   80.952
LGA    Y    15_A      Y    15_A     0.919     0    0.047   0.165     1.592   88.214   82.976
LGA    A    16_A      A    16_A     0.879     0    0.028   0.030     0.948   92.857   92.381
LGA    S    17_A      S    17_A     1.046     0    0.020   0.053     1.251   85.952   84.444
LGA    D    18_A      D    18_A     0.829     0    0.096   0.529     3.374   90.476   76.905
LGA    K    19_A      K    19_A     0.517     0    0.028   0.803     4.276   95.238   75.503
LGA    L    20_A      L    20_A     0.828     0    0.040   0.143     1.328   88.214   85.952
LGA    F    21_A      F    21_A     0.728     0    0.020   0.059     1.342   90.476   88.009
LGA    R    22_A      R    22_A     1.095     0    0.028   1.332     4.634   81.429   69.481
LGA    A    23_A      A    23_A     0.910     0    0.037   0.034     0.981   90.476   90.476
LGA    D    24_A      D    24_A     1.327     0    0.041   0.145     1.832   77.143   79.286
LGA    I    25_A      I    25_A     1.642     0    0.051   0.142     1.800   75.000   73.929
LGA    S    26_A      S    26_A     1.535     0    0.032   0.553     3.093   70.833   67.698
LGA    E    27_A      E    27_A     1.595     0    0.264   0.313     2.296   79.286   74.815
LGA    D    28_A      D    28_A     1.274     0    0.049   0.877     6.397   81.548   58.869
LGA    Y    29_A      Y    29_A     2.839     0    0.624   0.412     7.859   45.119   34.643
LGA    K    30_A      K    30_A     4.306     0    0.596   1.084    10.462   34.881   25.661
LGA    T    31_A      T    31_A     8.642     0    0.602   0.978    10.987    4.167    2.517
LGA    R    32_A      R    32_A    12.167     0    0.672   1.231    16.217    0.000    0.649
LGA    G    33_A      G    33_A    16.151     0    0.072   0.072    18.134    0.000    0.000
LGA    R    34_A      R    34_A    22.869     0    0.048   1.092    31.221    0.000    0.000
LGA    K    35_A      K    35_A    27.059     0    0.028   0.640    29.752    0.000    0.000
LGA    L    36_A      L    36_A    34.580     0    0.051   0.134    41.531    0.000    0.000
LGA    L    37_A      L    37_A    36.595     0    0.016   0.035    40.749    0.000    0.000
LGA    R    38_A      R    38_A    43.951     0    0.027   1.005    45.171    0.000    0.000
LGA    F    39_A      F    39_A    49.190     0    0.021   1.452    53.098    0.000    0.000
LGA    N    40_A      N    40_A    56.070     0    0.083   0.465    57.943    0.000    0.000
LGA    G    41_A      G    41_A    62.508     0    0.039   0.039    65.372    0.000    0.000
LGA    P    42_A      P    42_A    66.991     0    0.057   0.101    70.306    0.000    0.000
LGA    V    43_A      V    43_A    65.500     0    0.019   0.068    67.733    0.000    0.000
LGA    P    44_A      P    44_A    69.187     0    0.036   0.094    70.123    0.000    0.000
LGA    P    45_A      P    45_A    66.954     0    0.077   0.375    71.422    0.000    0.000
LGA    P    46_A      P    46_A    62.327     0    0.109   0.371    65.103    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       42     168    168  100.00     352    352  100.00                97
SUMMARY(RMSD_GDC):    23.841         23.943                 23.618           21.873   19.503

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   97    4.0     26    1.63    25.000    24.786     1.500

LGA_LOCAL      RMSD:   1.633  Number of atoms:   26  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  29.951  Number of assigned atoms:   42 
Std_ASGN_ATOMS RMSD:  23.841  Standard rmsd on all 42 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.164588 * X  +   0.894374 * Y  +  -0.415941 * Z  +  21.255669
  Y_new =  -0.979051 * X  +  -0.199382 * Y  +  -0.041309 * Z  +  -3.367288
  Z_new =  -0.119877 * X  +   0.400428 * Y  +   0.908453 * Z  +  11.498068 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.737349  0.120166  0.415160   [DEG:  -99.5428    6.8850   23.7869 ]
ZXZ: -1.471807  0.431228 -0.290879   [DEG:  -84.3283   24.7076  -16.6662 ]
 
# END of job
