
#######################################################
#                                                     #
#                        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        4.86     5.15
  LCS_AVERAGE:     97.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        1.79     5.56
  LCS_AVERAGE:     49.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      11_B - 28_B        0.98     5.89
  LONGEST_CONTINUOUS_SEGMENT:    18      12_B - 29_B        0.98     5.86
  LCS_AVERAGE:     29.64

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     16   28   42     12   13   15   20   22   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     L     6_B     L     6_B     16   28   42     12   13   15   20   22   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     E     7_B     E     7_B     16   28   42     12   13   16   20   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     T     8_B     T     8_B     16   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     K     9_B     K     9_B     17   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     K    10_B     K    10_B     17   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     A    11_B     A    11_B     18   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     Y    12_B     Y    12_B     18   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     A    13_B     A    13_B     18   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     A    14_B     A    14_B     18   28   42     12   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     R    15_B     R    15_B     18   28   42     12   13   17   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     T    16_B     T    16_B     18   28   42     12   13   16   20   24   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     R    17_B     R    17_B     18   28   42      6   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     R    18_B     R    18_B     18   28   42      6   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     S    19_B     S    19_B     18   28   42      6   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     N    20_B     N    20_B     18   28   42      6   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     Y    21_B     Y    21_B     18   28   42      7   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     A    22_B     A    22_B     18   28   42      7   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     A    23_B     A    23_B     18   28   42      7   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     S    24_B     S    24_B     18   28   42      7   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     L    25_B     L    25_B     18   28   42      7   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     R    26_B     R    26_B     18   28   42      6   13   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     L    27_B     L    27_B     18   28   42      5   12   17   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     E    28_B     E    28_B     18   28   42      6   12   17   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     G    29_B     G    29_B     18   28   42      3   10   17   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     F    30_B     F    30_B     16   28   42      3   11   18   22   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     K    31_B     K    31_B     15   28   42      3   10   14   21   25   27   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     V    32_B     V    32_B     15   28   42      3    8   14   21   25   26   28   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     T    33_B     T    33_B      5   23   42      4    4    5    6    8   19   24   27   29   31   31   32   34   35   38   39   40   40   41   41 
LCS_GDT     F    34_B     F    34_B      5    7   42      4    4    5    6    7    8    8   11   13   14   26   32   32   32   32   35   37   38   40   41 
LCS_GDT     A    35_B     A    35_B      5    7   42      4    4    5    6   11   19   23   27   29   31   31   32   32   34   36   37   39   40   41   41 
LCS_GDT     D    36_B     D    36_B      5    7   42      4    4    5    6    8    9   14   29   29   31   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     G    37_B     G    37_B      5    7   42      3    4    5    6    8    9   10   15   18   20   22   26   29   34   38   39   40   40   41   41 
LCS_GDT     E    38_B     E    38_B      4    8   42      3    4    4    6    8   14   17   21   29   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     R    39_B     R    39_B      4    8   42      3    5   14   17   19   22   24   26   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     K    40_B     K    40_B      3    8   42      3    5    6    6    9   10   23   25   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     M    41_B     M    41_B      4    8   42      3    4    7   14   18   21   26   29   31   32   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     P    42_B     P    42_B      4    8   42      3    5    6    6    9   14   19   23   25   28   34   34   35   36   38   39   40   40   41   41 
LCS_GDT     T    43_B     T    43_B      4    8   42      3    5    6    6   11   16   19   21   22   25   30   33   35   36   38   39   40   40   41   41 
LCS_GDT     R    44_B     R    44_B      4    8   42      3    5    6    6   13   16   19   21   22   25   30   33   34   36   38   39   40   40   41   41 
LCS_GDT     E    45_B     E    45_B      4    8   42      3    4    6    6   11   16   19   21   22   24   28   30   33   35   36   39   40   40   41   41 
LCS_GDT     E    46_B     E    46_B      3    8   42      3    3    3    3    4    4    8   11   21   24   24   25   31   32   34   37   40   40   41   41 
LCS_GDT     V    47_B     V    47_B      3    3   37      2    3    3    3    3    3    4    5    5   20   23   24   26   28   29   31   35   37   39   40 
LCS_AVERAGE  LCS_A:  58.75  (  29.64   49.22   97.40 )

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     12     13     18     22     25     27     28     29     31     32     34     34     35     36     38     39     40     40     41     41 
GDT PERCENT_AT  27.91  30.23  41.86  51.16  58.14  62.79  65.12  67.44  72.09  74.42  79.07  79.07  81.40  83.72  88.37  90.70  93.02  93.02  95.35  95.35
GDT RMS_LOCAL    0.31   0.62   1.02   1.27   1.56   1.72   1.79   1.94   2.33   2.46   2.79   2.79   3.05   3.34   3.78   4.07   4.30   4.30   4.56   4.56
GDT RMS_ALL_AT   7.95   5.96   5.65   5.60   5.51   5.61   5.56   5.58   5.64   5.64   5.51   5.51   5.45   5.37   5.29   5.21   5.20   5.20   5.16   5.16

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  E    38_B      E    38_B
#   possible swapping detected:  E    45_B      E    45_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.693     0    0.638   0.670     5.344   67.381   53.651
LGA    L     6_B      L     6_B     3.200     0    0.050   1.276     6.677   55.476   48.571
LGA    E     7_B      E     7_B     2.491     0    0.092   0.945     7.967   69.048   45.238
LGA    T     8_B      T     8_B     0.711     0    0.072   1.213     2.813   90.595   82.381
LGA    K     9_B      K     9_B     1.100     0    0.034   1.599     6.717   88.214   66.561
LGA    K    10_B      K    10_B     0.604     0    0.033   1.256     6.906   95.238   67.196
LGA    A    11_B      A    11_B     0.664     0    0.040   0.043     1.138   90.595   88.762
LGA    Y    12_B      Y    12_B     1.092     0    0.034   1.090     7.173   81.548   56.706
LGA    A    13_B      A    13_B     1.233     0    0.029   0.058     1.493   81.429   81.429
LGA    A    14_B      A    14_B     1.078     0    0.070   0.068     2.293   77.381   78.190
LGA    R    15_B      R    15_B     2.428     0    0.066   1.145     4.439   61.190   54.199
LGA    T    16_B      T    16_B     3.183     0    0.180   1.057     6.165   59.167   50.612
LGA    R    17_B      R    17_B     1.246     0    0.062   1.006     4.258   83.810   77.619
LGA    R    18_B      R    18_B     1.552     0    0.058   1.250     7.792   75.000   44.199
LGA    S    19_B      S    19_B     2.330     0    0.062   0.594     4.239   68.810   61.587
LGA    N    20_B      N    20_B     1.764     0    0.028   1.235     4.358   77.143   62.202
LGA    Y    21_B      Y    21_B     0.905     0    0.049   0.149     1.596   85.952   83.770
LGA    A    22_B      A    22_B     1.468     0    0.046   0.058     2.075   81.429   78.095
LGA    A    23_B      A    23_B     1.438     0    0.028   0.035     1.730   81.429   79.714
LGA    S    24_B      S    24_B     1.431     0    0.092   0.641     1.633   79.286   80.000
LGA    L    25_B      L    25_B     1.151     0    0.039   0.891     3.724   85.952   80.179
LGA    R    26_B      R    26_B     0.665     0    0.040   1.210     4.735   85.952   71.948
LGA    L    27_B      L    27_B     1.855     0    0.086   1.016     6.519   69.048   52.143
LGA    E    28_B      E    28_B     1.918     0    0.174   1.000     4.176   68.929   63.069
LGA    G    29_B      G    29_B     2.163     0    0.203   0.203     2.163   70.833   70.833
LGA    F    30_B      F    30_B     1.240     0    0.543   1.072     6.800   66.190   50.996
LGA    K    31_B      K    31_B     2.270     0    0.245   0.628     5.918   63.095   45.556
LGA    V    32_B      V    32_B     2.482     0    0.141   1.266     6.386   44.524   50.204
LGA    T    33_B      T    33_B     8.063     0    0.114   1.006    11.042   12.024    7.143
LGA    F    34_B      F    34_B    11.391     0    0.083   0.190    18.823    0.119    0.043
LGA    A    35_B      A    35_B     9.215     0    0.096   0.094    10.120    7.976    6.381
LGA    D    36_B      D    36_B     4.143     0    0.077   0.179     8.323   27.857   21.369
LGA    G    37_B      G    37_B     7.161     0    0.088   0.088     8.750   13.095   13.095
LGA    E    38_B      E    38_B     5.212     0    0.761   1.232     5.456   28.810   36.296
LGA    R    39_B      R    39_B     6.040     0    0.096   1.519    10.554   19.405    8.615
LGA    K    40_B      K    40_B     6.790     0    0.335   0.671    10.933   14.405    7.989
LGA    M    41_B      M    41_B     6.123     0    0.625   1.187     8.819   17.262   13.690
LGA    P    42_B      P    42_B     6.894     0    0.211   0.360     7.629   10.238   11.088
LGA    T    43_B      T    43_B     8.984     0    0.085   0.076     9.609    2.976    1.905
LGA    R    44_B      R    44_B     9.964     0    0.575   0.988    13.407    0.595    0.216
LGA    E    45_B      E    45_B    12.322     0    0.484   1.031    14.191    0.000    0.000
LGA    E    46_B      E    46_B    12.959     0    0.565   1.369    15.454    0.000    0.000
LGA    V    47_B      V    47_B    14.293     0    0.438   1.104    15.697    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):     5.138          5.000                  5.971           52.544   45.429

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     29    1.94    59.884    59.672     1.421

LGA_LOCAL      RMSD:   1.941  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.580  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   5.138  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.602718 * X  +   0.356260 * Y  +   0.714009 * Z  +  13.067224
  Y_new =  -0.476256 * X  +  -0.878555 * Y  +   0.036339 * Z  + -66.160133
  Z_new =   0.640243 * X  +  -0.318149 * Y  +   0.699192 * Z  +   9.158381 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.472868 -0.694815 -0.427024   [DEG: -141.6849  -39.8099  -24.4667 ]
ZXZ:  1.621646  0.796529  2.031977   [DEG:   92.9135   45.6378  116.4237 ]
 
# END of job
