
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       5_B - 47_B        3.60     3.60
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       5_B - 39_B        1.87     4.51
  LCS_AVERAGE:     74.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.79     4.25
  LCS_AVERAGE:     54.79

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     5_B     S     5_B     29   35   43      5   15   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   35   43     21   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   35   43     23   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   35   43     19   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   35   43     12   26   27   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   35   43      7   11   25   29   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     15   35   43      7   11   15   19   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     15   35   43      7   11   19   28   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     15   35   43      7   11   15   27   32   32   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     15   35   43      7   11   15   17   19   24   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     15   35   43      5   11   15   17   19   22   29   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     15   35   43      4   11   15   17   19   22   34   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     15   22   43      7   11   15   17   19   22   26   36   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     15   22   43      3   11   15   17   19   22   23   32   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     15   22   43      5   10   15   17   19   22   23   26   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     14   22   43      4    7   12   16   17   19   22   25   28   33   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     10   21   43      4    6   10   12   16   18   21   23   26   30   34   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   21   43      4    6    7   11   15   18   21   23   26   30   34   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   14   43      3    3    3    4    6    7    9   12   16   23   23   27   35   39   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3   22   31   33   34   39   39   40   42   42   42   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  76.33  (  54.79   74.20  100.00 )

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     23     26     27     29     32     32     34     36     39     39     40     42     42     42     43     43     43     43     43     43 
GDT PERCENT_AT  53.49  60.47  62.79  67.44  74.42  74.42  79.07  83.72  90.70  90.70  93.02  97.67  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.37   0.45   0.79   1.32   1.32   1.71   2.06   2.66   2.66   2.91   3.39   3.39   3.39   3.60   3.60   3.60   3.60   3.60   3.60
GDT RMS_ALL_AT   4.42   4.46   4.39   4.25   4.34   4.34   4.43   4.45   3.89   3.89   3.78   3.63   3.63   3.63   3.60   3.60   3.60   3.60   3.60   3.60

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.267     0    0.614   0.913     4.708   70.833   59.683
LGA    L     6_B      L     6_B     1.254     0    0.042   1.215     3.833   83.810   75.714
LGA    E     7_B      E     7_B     0.443     0    0.057   1.102     4.274   95.238   83.704
LGA    T     8_B      T     8_B     1.368     0    0.041   1.192     3.001   83.690   74.626
LGA    K     9_B      K     9_B     1.099     0    0.017   0.106     2.502   85.952   76.984
LGA    K    10_B      K    10_B     0.576     0    0.048   0.931     4.269   90.476   79.630
LGA    A    11_B      A    11_B     1.371     0    0.021   0.035     1.687   81.548   79.810
LGA    Y    12_B      Y    12_B     1.672     0    0.019   0.057     3.151   75.000   65.714
LGA    A    13_B      A    13_B     0.933     0    0.027   0.037     1.125   85.952   86.857
LGA    A    14_B      A    14_B     1.377     0    0.094   0.109     1.949   77.143   76.286
LGA    R    15_B      R    15_B     2.208     0    0.026   0.852     4.234   66.786   56.926
LGA    T    16_B      T    16_B     2.051     0    0.024   0.034     2.875   70.833   68.299
LGA    R    17_B      R    17_B     0.593     0    0.060   1.066     4.942   88.214   73.593
LGA    R    18_B      R    18_B     2.004     0    0.030   0.646     3.003   68.810   60.736
LGA    S    19_B      S    19_B     2.540     0    0.038   0.643     3.782   62.857   57.460
LGA    N    20_B      N    20_B     1.568     0    0.073   0.478     1.998   77.143   76.071
LGA    Y    21_B      Y    21_B     0.336     0    0.056   0.182     4.003   95.238   73.016
LGA    A    22_B      A    22_B     1.393     0    0.041   0.039     1.895   81.429   79.714
LGA    A    23_B      A    23_B     1.763     0    0.039   0.045     2.105   77.143   74.667
LGA    S    24_B      S    24_B     1.107     0    0.085   0.720     1.498   85.952   84.444
LGA    L    25_B      L    25_B     0.106     0    0.020   0.077     0.793  100.000   97.619
LGA    R    26_B      R    26_B     0.978     0    0.019   1.061     2.978   85.952   76.407
LGA    L    27_B      L    27_B     1.545     0    0.058   0.204     3.044   77.143   70.119
LGA    E    28_B      E    28_B     1.206     0    0.054   0.536     2.958   83.690   75.079
LGA    G    29_B      G    29_B     0.270     0    0.035   0.035     0.569   97.619   97.619
LGA    F    30_B      F    30_B     0.779     0    0.073   0.113     1.623   88.333   84.848
LGA    K    31_B      K    31_B     1.825     0    0.016   0.623     6.447   72.857   54.233
LGA    V    32_B      V    32_B     1.129     0    0.051   1.232     3.546   81.429   74.762
LGA    T    33_B      T    33_B     1.370     0    0.082   1.050     2.943   81.548   76.803
LGA    F    34_B      F    34_B     2.333     0    0.019   1.109     3.827   64.881   64.719
LGA    A    35_B      A    35_B     1.633     0    0.038   0.036     2.604   68.929   71.429
LGA    D    36_B      D    36_B     2.009     0    0.009   0.233     3.261   61.190   71.369
LGA    G    37_B      G    37_B     3.694     0    0.028   0.028     4.946   42.262   42.262
LGA    E    38_B      E    38_B     4.483     0    0.049   0.249     6.037   34.524   31.323
LGA    R    39_B      R    39_B     4.439     0    0.131   1.161     5.275   32.976   36.970
LGA    K    40_B      K    40_B     5.415     0    0.072   0.857     5.742   25.119   28.201
LGA    M    41_B      M    41_B     5.964     0    0.030   0.260     7.274   16.548   17.083
LGA    P    42_B      P    42_B     7.340     0    0.059   0.066     8.159    8.214   11.633
LGA    T    43_B      T    43_B     9.643     0    0.008   0.048    10.574    1.071    0.612
LGA    R    44_B      R    44_B    11.066     0    0.604   0.853    18.330    0.000    0.000
LGA    E    45_B      E    45_B    11.945     0    0.475   1.416    12.478    0.000    0.000
LGA    E    46_B      E    46_B    13.511     0    0.594   1.430    18.140    0.000    0.000
LGA    V    47_B      V    47_B     8.294     0    0.401   1.362    10.558    1.667   12.653

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     3.603          3.610                  4.144           63.488   59.527

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     36    2.06    77.907    78.720     1.663

LGA_LOCAL      RMSD:   2.064  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.452  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.603  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.416419 * X  +  -0.869401 * Y  +   0.265963 * Z  +  28.452005
  Y_new =  -0.602934 * X  +  -0.045123 * Y  +   0.796514 * Z  + -33.914333
  Z_new =  -0.680489 * X  +  -0.492042 * Y  +  -0.542982 * Z  +  19.825188 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.966370  0.748429 -2.405371   [DEG:  -55.3689   42.8818 -137.8176 ]
ZXZ:  2.819324  2.144781 -2.196839   [DEG:  161.5354  122.8869 -125.8696 ]
 
# END of job
