
#######################################################
#                                                     #
#                        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   56 (  447),  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        3.27     3.27
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       5_B - 41_B        1.90     4.16
  LCS_AVERAGE:     79.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.81     3.76
  LCS_AVERAGE:     54.41

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   37   43      5   24   28   28   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   37   43     25   27   28   29   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   37   43     24   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   37   43     25   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   37   43     11   27   28   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   37   43      6   13   26   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     15   37   43      6   13   19   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     15   37   43      6   13   24   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     15   37   43      6   13   20   30   32   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     15   37   43      6   13   15   18   27   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     15   37   43      6   13   15   18   25   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     15   37   43      6   13   15   18   27   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     15   37   43      4   13   15   18   25   34   36   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     15   37   43      4   11   14   17   19   22   30   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     14   24   43      4    7   11   15   18   22   28   38   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     11   23   43      4    7   11   13   16   19   23   34   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   20   43      4    6    9   12   13   16   19   24   28   38   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   15   43      4    6    7    9   13   13   15   17   26   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    3    6    6    8   10   14   16   18   26   31   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    3   29   34   37   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  77.84  (  54.41   79.12  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     25     27     28     30     32     34     36     38     40     41     42     42     42     43     43     43     43     43     43     43 
GDT PERCENT_AT  58.14  62.79  65.12  69.77  74.42  79.07  83.72  88.37  93.02  95.35  97.67  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.46   0.52   1.19   1.27   1.52   1.73   2.10   2.58   2.83   3.00   3.00   3.00   3.27   3.27   3.27   3.27   3.27   3.27   3.27
GDT RMS_ALL_AT   4.03   3.90   3.92   4.17   3.97   4.15   4.25   3.95   3.46   3.34   3.31   3.31   3.31   3.27   3.27   3.27   3.27   3.27   3.27   3.27

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   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:  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     2.209     0    0.599   0.878     4.508   68.810   59.444
LGA    L     6_B      L     6_B     1.110     0    0.052   1.231     3.869   88.333   79.048
LGA    E     7_B      E     7_B     0.677     0    0.039   0.707     3.527   90.595   79.471
LGA    T     8_B      T     8_B     1.756     0    0.035   1.197     3.541   75.000   67.551
LGA    K     9_B      K     9_B     1.039     0    0.021   0.116     2.778   85.952   76.984
LGA    K    10_B      K    10_B     0.780     0    0.026   0.927     4.735   88.333   76.138
LGA    A    11_B      A    11_B     1.808     0    0.016   0.016     2.151   72.976   71.333
LGA    Y    12_B      Y    12_B     1.823     0    0.025   0.064     3.210   72.857   64.405
LGA    A    13_B      A    13_B     0.766     0    0.023   0.023     1.039   88.214   88.667
LGA    A    14_B      A    14_B     1.771     0    0.070   0.079     2.316   72.976   71.333
LGA    R    15_B      R    15_B     2.527     0    0.054   0.802     4.390   60.952   51.039
LGA    T    16_B      T    16_B     2.155     0    0.023   0.096     2.808   68.810   67.143
LGA    R    17_B      R    17_B     0.865     0    0.041   1.268     5.043   85.952   72.857
LGA    R    18_B      R    18_B     1.955     0    0.008   0.689     3.035   70.833   62.165
LGA    S    19_B      S    19_B     2.439     0    0.055   0.672     3.494   64.762   61.032
LGA    N    20_B      N    20_B     1.583     0    0.053   0.462     1.885   77.143   78.214
LGA    Y    21_B      Y    21_B     0.618     0    0.046   0.187     3.362   90.476   75.754
LGA    A    22_B      A    22_B     1.469     0    0.030   0.029     1.848   81.429   79.714
LGA    A    23_B      A    23_B     1.667     0    0.038   0.038     1.924   77.143   76.286
LGA    S    24_B      S    24_B     0.988     0    0.065   0.683     1.647   88.214   86.032
LGA    L    25_B      L    25_B     0.501     0    0.033   0.064     0.687   92.857   94.048
LGA    R    26_B      R    26_B     0.996     0    0.026   1.068     4.763   88.214   69.654
LGA    L    27_B      L    27_B     1.158     0    0.031   0.187     2.433   81.429   77.202
LGA    E    28_B      E    28_B     0.614     0    0.042   1.053     5.017   92.857   77.037
LGA    G    29_B      G    29_B     0.443     0    0.024   0.024     0.604   97.619   97.619
LGA    F    30_B      F    30_B     0.653     0    0.061   0.121     1.000   92.857   93.983
LGA    K    31_B      K    31_B     1.394     0    0.024   0.624     5.620   81.429   61.481
LGA    V    32_B      V    32_B     0.721     0    0.059   1.207     3.359   85.952   78.435
LGA    T    33_B      T    33_B     1.286     0    0.033   1.001     3.440   83.690   78.231
LGA    F    34_B      F    34_B     2.130     0    0.016   1.380     3.868   66.786   62.424
LGA    A    35_B      A    35_B     1.690     0    0.018   0.019     2.088   70.833   72.952
LGA    D    36_B      D    36_B     1.607     0    0.012   0.090     2.393   68.810   79.702
LGA    G    37_B      G    37_B     2.933     0    0.021   0.021     3.596   53.810   53.810
LGA    E    38_B      E    38_B     3.464     0    0.058   0.342     4.952   48.333   44.286
LGA    R    39_B      R    39_B     3.185     0    0.163   1.159     4.574   46.786   49.351
LGA    K    40_B      K    40_B     3.556     0    0.102   1.210     6.589   40.476   42.910
LGA    M    41_B      M    41_B     4.742     0    0.019   0.996     8.634   32.857   26.131
LGA    P    42_B      P    42_B     5.680     0    0.029   0.046     6.587   19.524   21.020
LGA    T    43_B      T    43_B     7.314     0    0.025   0.141     7.883    9.405    9.252
LGA    R    44_B      R    44_B     9.280     0    0.605   0.977    16.397    1.190    0.476
LGA    E    45_B      E    45_B    10.463     0    0.461   1.498    11.151    0.119    1.058
LGA    E    46_B      E    46_B    13.307     0    0.586   1.450    17.016    0.000    0.000
LGA    V    47_B      V    47_B     8.834     0    0.415   1.378    11.282    0.714    9.592

# 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):     3.271          3.292                  3.796           65.728   61.518

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     38    2.10    80.233    81.827     1.726

LGA_LOCAL      RMSD:   2.102  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.953  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.271  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.563886 * X  +  -0.717010 * Y  +  -0.409792 * Z  +  24.032263
  Y_new =  -0.553021 * X  +  -0.040693 * Y  +   0.832173 * Z  + -31.744307
  Z_new =  -0.613352 * X  +   0.695874 * Y  +  -0.373575 * Z  +  19.458349 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.365922  0.660298  2.063482   [DEG: -135.5574   37.8323  118.2288 ]
ZXZ: -2.684015  1.953656 -0.722450   [DEG: -153.7827  111.9363  -41.3933 ]
 
# END of job
