
#######################################################
#                                                     #
#                        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:    42       5_B - 46_B        4.63     5.10
  LCS_AVERAGE:     97.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        1.74     5.31
  LCS_AVERAGE:     49.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       6_B - 29_B        0.90     5.65
  LONGEST_CONTINUOUS_SEGMENT:    24       7_B - 30_B        0.97     5.38
  LCS_AVERAGE:     39.70

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     23   28   42      5    9   13   21   25   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     L     6_B     L     6_B     24   28   42      5   11   22   24   25   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     E     7_B     E     7_B     24   28   42      5   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     T     8_B     T     8_B     24   28   42      5   18   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     K     9_B     K     9_B     24   28   42      5   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     K    10_B     K    10_B     24   28   42     12   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     A    11_B     A    11_B     24   28   42     12   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     Y    12_B     Y    12_B     24   28   42     12   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     A    13_B     A    13_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     A    14_B     A    14_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     R    15_B     R    15_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     T    16_B     T    16_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     R    17_B     R    17_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     R    18_B     R    18_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     S    19_B     S    19_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     N    20_B     N    20_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     Y    21_B     Y    21_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     A    22_B     A    22_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     A    23_B     A    23_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     S    24_B     S    24_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     L    25_B     L    25_B     24   28   42     13   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     R    26_B     R    26_B     24   28   42     11   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     L    27_B     L    27_B     24   28   42     12   20   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     E    28_B     E    28_B     24   28   42      8   19   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     G    29_B     G    29_B     24   28   42      8   19   23   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     F    30_B     F    30_B     24   28   42      4   15   20   24   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     K    31_B     K    31_B     20   28   42      4   14   18   22   26   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     V    32_B     V    32_B     19   28   42      3    6   18   22   26   27   28   28   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     T    33_B     T    33_B      6   25   42      4    5    6    7   10   17   21   25   26   29   30   32   32   34   37   38   39   41   42   42 
LCS_GDT     F    34_B     F    34_B      6    9   42      4    5    6    7    9   13   18   21   25   27   29   31   32   33   37   37   39   39   42   42 
LCS_GDT     A    35_B     A    35_B      6    9   42      4    5    7   16   20   23   28   28   29   30   31   32   33   35   37   38   39   41   42   42 
LCS_GDT     D    36_B     D    36_B      6    9   42      4   12   18   22   26   27   28   28   29   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     G    37_B     G    37_B      5    9   42      3    4    5    5    7   12   16   22   29   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     E    38_B     E    38_B      4    7   42      3    3    4    5    7    7   13   17   22   26   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     R    39_B     R    39_B      4    7   42      3    3    4   13   25   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     K    40_B     K    40_B      4    7   42      3    3    4    5    6    7   13   15   28   29   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     M    41_B     M    41_B      5    7   42      4    5    5    5    8   27   28   29   30   32   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     P    42_B     P    42_B      5    7   42      4    5    5    5    8   11   25   26   28   31   35   35   36   36   37   38   39   41   42   42 
LCS_GDT     T    43_B     T    43_B      5    7   42      4    5    5    5    8   10   17   20   23   29   30   33   36   36   37   38   39   41   42   42 
LCS_GDT     R    44_B     R    44_B      5    6   42      4    5    5    5    6    6    8   15   18   22   24   29   30   31   33   38   39   41   42   42 
LCS_GDT     E    45_B     E    45_B      5    6   42      3    5    5    5    6    6    8    9   12   22   23   29   30   31   33   37   39   41   42   42 
LCS_GDT     E    46_B     E    46_B      3    6   42      3    3    3    3    4    6    6    7    8   14   23   26   30   30   37   38   39   41   42   42 
LCS_GDT     V    47_B     V    47_B      3    3   38      0    3    3    3    3    3    4    6    7    7    7    9    9    9   20   24   25   29   30   35 
LCS_AVERAGE  LCS_A:  62.09  (  39.70   49.11   97.46 )

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     13     20     23     24     26     27     28     29     30     32     35     35     36     36     37     38     39     41     42     42 
GDT PERCENT_AT  30.23  46.51  53.49  55.81  60.47  62.79  65.12  67.44  69.77  74.42  81.40  81.40  83.72  83.72  86.05  88.37  90.70  95.35  97.67  97.67
GDT RMS_LOCAL    0.31   0.59   0.78   0.90   1.49   1.27   1.40   1.66   1.89   2.29   2.73   2.73   2.94   2.94   3.31   3.60   3.91   4.38   4.63   4.63
GDT RMS_ALL_AT   5.40   5.54   5.51   5.65   5.26   5.86   5.77   5.62   5.49   5.32   5.32   5.32   5.28   5.28   5.20   5.19   5.21   5.10   5.10   5.10

# Checking swapping
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     3.089     0    0.646   0.685     5.197   53.452   55.000
LGA    L     6_B      L     6_B     2.251     0    0.041   0.862     3.359   71.190   65.179
LGA    E     7_B      E     7_B     0.989     0    0.116   0.968     2.362   88.214   78.836
LGA    T     8_B      T     8_B     0.997     0    0.080   0.995     3.855   92.976   82.585
LGA    K     9_B      K     9_B     0.853     0    0.046   1.319     8.229   88.214   56.720
LGA    K    10_B      K    10_B     0.614     0    0.021   0.890     4.062   90.476   75.132
LGA    A    11_B      A    11_B     0.826     0    0.051   0.051     0.979   90.476   90.476
LGA    Y    12_B      Y    12_B     1.180     0    0.023   0.111     2.625   83.690   73.849
LGA    A    13_B      A    13_B     1.101     0    0.032   0.103     1.235   83.690   83.238
LGA    A    14_B      A    14_B     0.655     0    0.076   0.073     0.848   90.476   90.476
LGA    R    15_B      R    15_B     1.291     0    0.102   1.078     5.040   81.429   70.303
LGA    T    16_B      T    16_B     1.200     0    0.095   1.056     3.293   81.429   75.714
LGA    R    17_B      R    17_B     1.037     0    0.039   1.055     2.702   85.952   82.771
LGA    R    18_B      R    18_B     0.306     0    0.038   1.420     4.788   97.619   69.827
LGA    S    19_B      S    19_B     0.580     0    0.051   0.696     2.647   92.857   86.508
LGA    N    20_B      N    20_B     0.801     0    0.082   1.140     3.213   88.214   79.940
LGA    Y    21_B      Y    21_B     0.598     0    0.038   0.302     3.519   95.238   76.786
LGA    A    22_B      A    22_B     0.297     0    0.036   0.046     0.447  100.000  100.000
LGA    A    23_B      A    23_B     0.893     0    0.037   0.045     1.066   90.476   88.667
LGA    S    24_B      S    24_B     0.976     0    0.043   0.044     1.209   88.214   87.460
LGA    L    25_B      L    25_B     0.430     0    0.094   0.096     0.615   95.238   96.429
LGA    R    26_B      R    26_B     0.666     0    0.065   1.185     7.185   92.857   61.515
LGA    L    27_B      L    27_B     1.651     0    0.084   0.101     2.680   75.000   68.929
LGA    E    28_B      E    28_B     1.707     0    0.092   0.871     2.540   77.143   70.317
LGA    G    29_B      G    29_B     0.996     0    0.091   0.091     2.532   77.738   77.738
LGA    F    30_B      F    30_B     2.791     0    0.040   0.205     5.114   59.286   49.048
LGA    K    31_B      K    31_B     4.708     0    0.354   0.923     6.216   27.976   29.471
LGA    V    32_B      V    32_B     5.491     0    0.079   1.276     8.741   15.595   32.653
LGA    T    33_B      T    33_B    11.337     0    0.087   0.996    15.386    1.071    0.612
LGA    F    34_B      F    34_B    12.717     0    0.079   0.093    16.669    0.000    0.000
LGA    A    35_B      A    35_B    11.575     0    0.119   0.117    13.347    2.143    1.714
LGA    D    36_B      D    36_B     6.702     0    0.482   0.537    10.580   21.429   12.143
LGA    G    37_B      G    37_B     6.001     0    0.618   0.618     6.001   20.357   20.357
LGA    E    38_B      E    38_B     6.107     0    0.152   0.875    11.327   22.857   12.222
LGA    R    39_B      R    39_B     2.452     0    0.614   1.460     7.525   55.476   46.017
LGA    K    40_B      K    40_B     5.705     0    0.440   1.358    13.725   27.857   12.698
LGA    M    41_B      M    41_B     2.854     0    0.630   0.765     7.782   48.690   36.667
LGA    P    42_B      P    42_B     5.218     0    0.048   0.504     6.146   24.405   31.973
LGA    T    43_B      T    43_B     7.535     0    0.045   0.046     9.052    6.548    6.054
LGA    R    44_B      R    44_B    10.637     0    0.573   1.232    13.973    0.357    0.130
LGA    E    45_B      E    45_B    12.205     0    0.447   1.155    13.720    0.000    0.000
LGA    E    46_B      E    46_B     9.539     0    0.574   1.581    12.083    0.119    5.714
LGA    V    47_B      V    47_B    15.313     0    0.483   1.315    17.105    0.000    0.000

# 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):     5.091          5.010                  5.776           57.824   52.136

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     29    1.66    64.535    62.318     1.645

LGA_LOCAL      RMSD:   1.663  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.618  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   5.091  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.988090 * X  +   0.146207 * Y  +  -0.047979 * Z  +  15.798420
  Y_new =  -0.153467 * X  +  -0.913552 * Y  +   0.376656 * Z  + -68.751526
  Z_new =   0.011238 * X  +   0.379533 * Y  +   0.925110 * Z  +  16.508308 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.987507 -0.011238  0.389318   [DEG: -171.1715   -0.6439   22.3063 ]
ZXZ: -3.014893  0.389472  0.029602   [DEG: -172.7407   22.3151    1.6961 ]
 
# END of job
