
#######################################################
#                                                     #
#                        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        3.43     3.43
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       5_B - 38_B        1.85     4.15
  LONGEST_CONTINUOUS_SEGMENT:    34       6_B - 39_B        1.99     4.27
  LCS_AVERAGE:     71.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.91     4.08
  LCS_AVERAGE:     54.03

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   34   43      5   19   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   34   43     19   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   34   43     19   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   34   43     20   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   34   43     19   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   34   43     19   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   34   43     21   26   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   34   43      8   25   27   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   34   43      6   10   21   28   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     14   34   43      6   10   14   22   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     14   34   43      6   10   16   26   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     14   34   43      6   10   14   24   31   32   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     14   34   43      6   10   14   16   19   25   33   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     14   34   43      4   10   14   16   19   21   28   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     14   34   43      4   10   14   16   19   21   29   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     14   22   43      6   10   14   16   19   21   26   36   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     14   22   43      3   10   14   16   19   21   23   35   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     14   22   43      4    8   14   15   19   20   23   29   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     11   21   43      4    7   11   14   16   19   22   26   38   40   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   20   43      4    6    9   12   13   17   20   22   26   32   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   16   43      4    5    7   10   13   14   17   21   22   28   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    3    6    9    9   11   14   21   24   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3   26   29   32   33   34   39   40   42   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  75.23  (  54.03   71.66  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     21     26     27     28     31     32     33     36     39     40     42     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  48.84  60.47  62.79  65.12  72.09  74.42  76.74  83.72  90.70  93.02  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.41   0.50   0.61   1.42   1.45   1.63   2.17   2.65   2.83   3.22   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43
GDT RMS_ALL_AT   4.41   4.52   4.53   4.37   4.02   4.01   4.05   4.17   3.67   3.59   3.45   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43

# 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     2.472     0    0.607   0.903     4.806   70.833   59.683
LGA    L     6_B      L     6_B     1.511     0    0.060   1.233     4.177   81.667   73.869
LGA    E     7_B      E     7_B     0.628     0    0.069   0.510     2.946   90.476   78.995
LGA    T     8_B      T     8_B     1.467     0    0.050   1.190     3.062   81.548   72.245
LGA    K     9_B      K     9_B     1.193     0    0.019   0.089     2.894   85.952   75.238
LGA    K    10_B      K    10_B     0.714     0    0.039   0.862     3.960   90.476   79.312
LGA    A    11_B      A    11_B     1.516     0    0.028   0.042     1.846   75.000   74.571
LGA    Y    12_B      Y    12_B     1.810     0    0.018   0.062     3.451   72.857   63.175
LGA    A    13_B      A    13_B     0.910     0    0.017   0.028     1.142   85.952   86.857
LGA    A    14_B      A    14_B     1.541     0    0.054   0.064     2.060   72.976   72.952
LGA    R    15_B      R    15_B     2.461     0    0.038   0.801     4.318   64.881   55.541
LGA    T    16_B      T    16_B     2.307     0    0.032   0.043     3.164   68.810   64.966
LGA    R    17_B      R    17_B     0.706     0    0.037   1.063     5.382   85.952   70.736
LGA    R    18_B      R    18_B     2.265     0    0.021   0.622     3.000   66.786   60.000
LGA    S    19_B      S    19_B     2.866     0    0.032   0.641     4.085   60.952   55.159
LGA    N    20_B      N    20_B     1.744     0    0.056   0.488     2.296   77.143   73.988
LGA    Y    21_B      Y    21_B     0.354     0    0.056   0.176     3.840   92.857   73.333
LGA    A    22_B      A    22_B     1.610     0    0.066   0.064     2.153   75.000   72.952
LGA    A    23_B      A    23_B     1.953     0    0.030   0.035     2.351   72.857   71.238
LGA    S    24_B      S    24_B     1.150     0    0.075   0.132     1.323   85.952   84.444
LGA    L    25_B      L    25_B     0.069     0    0.021   0.064     0.947  100.000   95.238
LGA    R    26_B      R    26_B     1.069     0    0.019   1.006     4.345   83.690   75.974
LGA    L    27_B      L    27_B     1.663     0    0.057   0.232     3.367   75.000   68.095
LGA    E    28_B      E    28_B     1.272     0    0.070   0.523     3.016   81.429   74.180
LGA    G    29_B      G    29_B     0.250     0    0.032   0.032     0.578   97.619   97.619
LGA    F    30_B      F    30_B     0.804     0    0.085   0.135     1.826   88.333   84.848
LGA    K    31_B      K    31_B     2.019     0    0.022   0.622     7.565   68.810   47.513
LGA    V    32_B      V    32_B     0.945     0    0.042   1.147     3.199   83.690   77.007
LGA    T    33_B      T    33_B     1.326     0    0.088   1.075     3.231   79.405   74.558
LGA    F    34_B      F    34_B     2.255     0    0.034   1.126     3.912   66.786   63.983
LGA    A    35_B      A    35_B     1.782     0    0.049   0.046     2.697   66.905   69.810
LGA    D    36_B      D    36_B     2.125     0    0.027   0.140     3.270   61.190   71.369
LGA    G    37_B      G    37_B     3.851     0    0.022   0.022     4.945   40.476   40.476
LGA    E    38_B      E    38_B     4.750     0    0.020   0.780     6.690   31.548   26.772
LGA    R    39_B      R    39_B     4.620     0    0.147   1.255     5.834   31.548   34.459
LGA    K    40_B      K    40_B     5.209     0    0.080   1.207     6.493   26.310   28.360
LGA    M    41_B      M    41_B     5.599     0    0.024   0.321     6.573   20.476   20.536
LGA    P    42_B      P    42_B     6.612     0    0.062   0.065     7.321   12.619   15.782
LGA    T    43_B      T    43_B     8.406     0    0.008   0.065     9.137    4.881    3.605
LGA    R    44_B      R    44_B     9.809     0    0.601   0.876    16.615    0.476    0.173
LGA    E    45_B      E    45_B    10.767     0    0.471   1.602    11.094    0.000    1.005
LGA    E    46_B      E    46_B    12.806     0    0.595   1.439    17.428    0.000    0.000
LGA    V    47_B      V    47_B     7.556     0    0.414   1.366     9.646    2.976   16.054

# 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):     3.427          3.421                  3.918           62.398   58.295

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     36    2.17    77.326    78.135     1.587

LGA_LOCAL      RMSD:   2.169  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.172  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.427  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.613101 * X  +   0.115465 * Y  +   0.781521 * Z  +  24.016037
  Y_new =  -0.766332 * X  +  -0.153434 * Y  +   0.623853 * Z  + -33.608566
  Z_new =   0.191945 * X  +  -0.981390 * Y  +  -0.005586 * Z  +  20.873154 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.896028 -0.193143 -1.576488   [DEG:  -51.3386  -11.0663  -90.3261 ]
ZXZ:  2.244473  1.576382  2.948446   [DEG:  128.5988   90.3201  168.9335 ]
 
# END of job
