
#######################################################
#                                                     #
#                        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        4.40     4.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      10_B - 33_B        1.90     5.97
  LONGEST_CONTINUOUS_SEGMENT:    24      11_B - 34_B        1.98     5.81
  LONGEST_CONTINUOUS_SEGMENT:    24      12_B - 35_B        1.97     6.04
  LCS_AVERAGE:     44.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      16_B - 33_B        0.79     7.35
  LCS_AVERAGE:     30.23

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     14   20   43     11   12   14   17   19   21   24   30   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     14   20   43     11   12   14   17   19   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     14   20   43     11   12   14   17   19   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     14   20   43     11   12   14   17   20   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     14   22   43     11   12   14   17   20   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     14   24   43     11   12   14   17   20   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     14   24   43     11   12   14   17   20   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     14   24   43     11   12   14   17   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     14   24   43     11   12   14   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     14   24   43     11   12   15   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     17   24   43     11   12   14   18   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     18   24   43     14   17   18   20   22   24   27   30   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     18   24   43     14   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     18   24   43      8   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     18   24   43      3   17   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     18   24   43      3    6   18   20   22   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B      4   24   43      3    4    5    5   13   22   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B      4   24   43      3    4    7   10   16   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B      4    6   43      3    4    5    5    5   10   10   10   13   22   28   34   35   37   41   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B      4    8   43      3    4    5    5    8   10   10   11   21   27   32   34   37   40   41   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B      7    8   43      3    5    9   15   20   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B      7    8   43      3    6    9   14   20   24   27   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B      7    8   43      3    6    9   15   17   21   24   32   33   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      7    8   43      3    9   13   17   19   21   22   25   30   35   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      7    8   43      4    6   14   17   19   20   22   25   29   33   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      7    8   43      4    6    9   16   19   20   22   25   28   33   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7    8   43      4    8    9   12   15   20   22   23   28   29   36   37   40   40   41   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7    8   43      4    5    7   16   19   20   22   25   29   33   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    8   43      3    3    3    5    5    5   19   20   28   34   36   39   40   40   41   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    3    3    4    5    7   20   24   27   30   37   39   41   43   43   43   43 
LCS_AVERAGE  LCS_A:  58.10  (  30.23   44.08  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     14     17     18     20     22     24     27     32     33     35     36     39     40     40     41     42     43     43     43     43 
GDT PERCENT_AT  32.56  39.53  41.86  46.51  51.16  55.81  62.79  74.42  76.74  81.40  83.72  90.70  93.02  93.02  95.35  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.59   0.79   1.25   1.54   1.90   2.20   2.69   2.76   2.99   3.17   3.69   3.82   3.82   4.00   4.20   4.40   4.40   4.40   4.40
GDT RMS_ALL_AT   7.53   7.50   7.35   6.72   6.26   5.97   5.55   5.04   5.06   4.90   4.74   4.47   4.44   4.44   4.42   4.41   4.40   4.40   4.40   4.40

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  D    36_B      D    36_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     5.038     0    0.628   0.935     8.877   34.405   24.603
LGA    L     6_B      L     6_B     4.040     0    0.045   1.217     5.809   43.929   43.036
LGA    E     7_B      E     7_B     3.332     0    0.037   0.840     6.805   53.810   38.624
LGA    T     8_B      T     8_B     2.344     0    0.042   1.210     5.199   69.048   58.503
LGA    K     9_B      K     9_B     1.953     0    0.011   0.158     4.516   75.119   57.725
LGA    K    10_B      K    10_B     0.843     0    0.015   0.941     5.357   90.595   73.069
LGA    A    11_B      A    11_B     1.398     0    0.011   0.013     1.994   81.548   79.810
LGA    Y    12_B      Y    12_B     1.186     0    0.016   1.224     8.619   75.476   49.167
LGA    A    13_B      A    13_B     2.105     0    0.011   0.012     2.988   64.881   66.476
LGA    A    14_B      A    14_B     2.437     0    0.080   0.086     4.123   56.190   57.905
LGA    R    15_B      R    15_B     3.720     0    0.049   1.206     4.985   40.476   52.900
LGA    T    16_B      T    16_B     4.642     0    0.202   1.070     7.000   37.262   33.401
LGA    R    17_B      R    17_B     3.313     0    0.040   0.790     7.351   50.119   31.818
LGA    R    18_B      R    18_B     3.046     0    0.007   1.119     5.920   51.786   39.697
LGA    S    19_B      S    19_B     3.950     0    0.043   0.716     4.785   45.000   41.429
LGA    N    20_B      N    20_B     3.374     0    0.024   0.325     4.591   53.810   47.083
LGA    Y    21_B      Y    21_B     1.333     0    0.065   0.104     3.035   79.524   78.413
LGA    A    22_B      A    22_B     1.767     0    0.011   0.017     2.583   75.000   71.429
LGA    A    23_B      A    23_B     2.140     0    0.017   0.018     2.917   68.810   66.476
LGA    S    24_B      S    24_B     1.812     0    0.062   0.716     2.108   75.000   75.873
LGA    L    25_B      L    25_B     0.586     0    0.041   0.085     1.013   88.214   92.917
LGA    R    26_B      R    26_B     0.333     0    0.044   1.006     5.299   92.976   67.056
LGA    L    27_B      L    27_B     1.657     0    0.048   0.225     2.506   71.071   68.929
LGA    E    28_B      E    28_B     2.239     0    0.092   1.048     5.175   64.881   55.344
LGA    G    29_B      G    29_B     2.493     0    0.105   0.105     2.751   62.857   62.857
LGA    F    30_B      F    30_B     2.264     0    0.103   0.120     3.514   60.952   59.481
LGA    K    31_B      K    31_B     3.237     0    0.201   0.856     9.839   51.786   30.635
LGA    V    32_B      V    32_B     3.143     0    0.586   1.141     5.313   42.381   47.483
LGA    T    33_B      T    33_B     2.341     0    0.205   0.974     3.649   57.500   64.354
LGA    F    34_B      F    34_B     4.030     0    0.092   1.463     6.632   40.476   29.567
LGA    A    35_B      A    35_B     3.717     0    0.307   0.325     6.269   34.762   39.238
LGA    D    36_B      D    36_B     8.654     0    0.030   1.058    11.193    4.881    2.917
LGA    G    37_B      G    37_B     7.744     0    0.662   0.662     7.744   15.476   15.476
LGA    E    38_B      E    38_B     1.941     0    0.479   1.297     6.347   61.548   45.820
LGA    R    39_B      R    39_B     2.291     0    0.454   1.233     5.121   53.929   52.771
LGA    K    40_B      K    40_B     4.676     0    0.407   1.140     5.863   34.405   36.561
LGA    M    41_B      M    41_B     6.352     0    0.040   0.294     7.299   14.643   16.488
LGA    P    42_B      P    42_B     8.496     0    0.035   0.047     8.959    4.405    4.354
LGA    T    43_B      T    43_B     9.799     0    0.034   0.047    10.505    0.476    0.340
LGA    R    44_B      R    44_B    11.009     0    0.591   1.396    16.675    0.000    0.000
LGA    E    45_B      E    45_B    10.853     0    0.472   1.140    11.243    0.119    0.106
LGA    E    46_B      E    46_B     7.801     0    0.608   1.408    11.399    2.976    4.127
LGA    V    47_B      V    47_B    13.095     0    0.435   1.394    15.702    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):     4.402          4.440                  5.026           48.430   43.820

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     32    2.69    64.535    60.316     1.147

LGA_LOCAL      RMSD:   2.689  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.042  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.402  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.355512 * X  +  -0.615190 * Y  +  -0.703671 * Z  +  26.453568
  Y_new =   0.602013 * X  +  -0.726608 * Y  +   0.331091 * Z  + -58.701923
  Z_new =  -0.714977 * X  +  -0.305912 * Y  +   0.628670 * Z  +  21.218040 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.104230  0.796591 -0.452872   [DEG:  120.5635   45.6413  -25.9476 ]
ZXZ: -2.010583  0.890954 -1.975089   [DEG: -115.1979   51.0479 -113.1643 ]
 
# END of job
