
#######################################################
#                                                     #
#                        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   35 (  277),  selected   35 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      25_A - 59_A        2.71     2.71
  LCS_AVERAGE:     58.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      30_A - 59_A        1.98     2.81
  LCS_AVERAGE:     46.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      28_A - 41_A        0.99     3.67
  LONGEST_CONTINUOUS_SEGMENT:    14      29_A - 42_A        0.80     3.60
  LONGEST_CONTINUOUS_SEGMENT:    14      46_A - 59_A        0.75     3.37
  LCS_AVERAGE:     20.38

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     V    25_A     V    25_A      3    3   35      0    3    3    3    3    6    6   14   17   21   32   34   35   35   35   35   35   35   35   35 
LCS_GDT     P    26_A     P    26_A      4   19   35      3    3    4   12   17   19   27   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     Q    27_A     Q    27_A      4   19   35      3    4    4   12   17   19   27   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     K    28_A     K    28_A     14   19   35      3    4   10   14   17   19   26   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     L    29_A     L    29_A     14   19   35      7   11   14   16   25   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     K    30_A     K    30_A     14   30   35      9   11   14   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     R    31_A     R    31_A     14   30   35      9   11   14   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     A    32_A     A    32_A     14   30   35      9   11   14   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     L    33_A     L    33_A     14   30   35      9   11   14   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     K    34_A     K    34_A     14   30   35      9   12   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     I    35_A     I    35_A     14   30   35      9   11   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     A    36_A     A    36_A     14   30   35      9   11   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     E    37_A     E    37_A     14   30   35      9   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     R    38_A     R    38_A     14   30   35      9   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     E    39_A     E    39_A     14   30   35      5   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     Q    40_A     Q    40_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     G    41_A     G    41_A     14   30   35      4   11   16   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     E    42_A     E    42_A     14   30   35      4    5   14   16   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     G    43_A     G    43_A      3   30   35      3    3    3   14   17   25   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     E    44_A     E    44_A      4   30   35      3    4   12   15   22   25   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     F    45_A     F    45_A      4   30   35      3    4    4    5    9   18   30   31   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     D    46_A     D    46_A     14   30   35      4   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     E    47_A     E    47_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     C    48_A     C    48_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     L    49_A     L    49_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     E    50_A     E    50_A     14   30   35     10   14   19   22   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     A    51_A     A    51_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     L    52_A     L    52_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     D    53_A     D    53_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     D    54_A     D    54_A     14   30   35     10   13   19   22   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     A    55_A     A    55_A     14   30   35     10   13   19   22   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     K    56_A     K    56_A     14   30   35     10   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     R    57_A     R    57_A     14   30   35      5   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     A    58_A     A    58_A     14   30   35      5   14   19   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_GDT     L    59_A     L    59_A     14   30   35      5   11   17   23   27   28   30   33   34   34   34   34   35   35   35   35   35   35   35   35 
LCS_AVERAGE  LCS_A:  41.78  (  20.38   46.62   58.33 )

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     10     14     19     23     27     28     30     33     34     34     34     34     35     35     35     35     35     35     35     35 
GDT PERCENT_AT  16.67  23.33  31.67  38.33  45.00  46.67  50.00  55.00  56.67  56.67  56.67  56.67  58.33  58.33  58.33  58.33  58.33  58.33  58.33  58.33
GDT RMS_LOCAL    0.27   0.60   0.86   1.36   1.54   1.64   1.91   2.35   2.45   2.45   2.45   2.45   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71
GDT RMS_ALL_AT   3.81   3.27   3.30   2.85   2.87   2.83   2.77   2.73   2.74   2.74   2.74   2.74   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71

# Checking swapping
#   possible swapping detected:  D    54_A      D    54_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    25_A      V    25_A     7.562     0    0.596   0.692    12.106   21.667   12.449
LGA    P    26_A      P    26_A     4.226     0    0.677   0.582     7.713   32.976   23.197
LGA    Q    27_A      Q    27_A     4.420     0    0.212   1.247     9.433   35.714   23.228
LGA    K    28_A      K    28_A     4.719     0    0.105   0.704     8.790   34.286   24.127
LGA    L    29_A      L    29_A     2.917     0    0.211   0.911     5.423   59.167   49.524
LGA    K    30_A      K    30_A     1.825     0    0.096   0.129     2.485   70.833   69.259
LGA    R    31_A      R    31_A     1.603     0    0.057   0.907     2.277   75.000   75.325
LGA    A    32_A      A    32_A     1.740     0    0.017   0.022     2.035   72.857   71.238
LGA    L    33_A      L    33_A     1.755     0    0.047   0.071     2.345   77.143   70.952
LGA    K    34_A      K    34_A     0.782     0    0.059   1.153     4.132   88.214   72.593
LGA    I    35_A      I    35_A     1.192     0    0.063   0.107     1.509   81.429   80.357
LGA    A    36_A      A    36_A     1.332     0    0.042   0.049     1.340   81.429   81.429
LGA    E    37_A      E    37_A     1.144     0    0.012   0.150     1.189   83.690   82.434
LGA    R    38_A      R    38_A     0.794     0    0.035   1.486     6.398   90.476   65.022
LGA    E    39_A      E    39_A     1.089     0    0.172   1.131     3.387   81.548   77.037
LGA    Q    40_A      Q    40_A     1.004     0    0.183   1.219     4.291   85.952   73.862
LGA    G    41_A      G    41_A     1.217     0    0.122   0.122     1.961   79.405   79.405
LGA    E    42_A      E    42_A     2.602     0    0.685   0.583    11.532   66.905   35.291
LGA    G    43_A      G    43_A     3.609     0    0.651   0.651     3.609   57.738   57.738
LGA    E    44_A      E    44_A     3.847     0    0.392   0.613     7.390   37.500   28.783
LGA    F    45_A      F    45_A     4.712     0    0.093   0.288     9.773   35.833   17.879
LGA    D    46_A      D    46_A     2.174     0    0.231   0.224     4.946   64.881   53.452
LGA    E    47_A      E    47_A     2.439     0    0.116   1.079     3.149   68.810   64.180
LGA    C    48_A      C    48_A     1.363     0    0.039   0.654     2.470   79.286   77.222
LGA    L    49_A      L    49_A     1.692     0    0.106   0.169     2.709   72.857   68.869
LGA    E    50_A      E    50_A     2.475     0    0.083   0.745     3.358   64.762   67.884
LGA    A    51_A      A    51_A     1.974     0    0.019   0.000     2.020   70.833   71.238
LGA    L    52_A      L    52_A     0.836     0    0.060   1.396     3.503   83.690   76.964
LGA    D    53_A      D    53_A     1.849     0    0.019   0.855     6.275   69.048   54.821
LGA    D    54_A      D    54_A     2.966     0    0.046   0.356     3.721   53.690   51.012
LGA    A    55_A      A    55_A     2.625     0    0.233   0.240     2.813   64.881   63.333
LGA    K    56_A      K    56_A     1.727     0    0.034   0.962     3.102   72.857   67.672
LGA    R    57_A      R    57_A     1.512     0    0.110   1.385     5.248   72.857   63.377
LGA    A    58_A      A    58_A     1.882     0    0.056   0.063     2.243   72.857   71.238
LGA    L    59_A      L    59_A     1.950     0    0.092   0.118     2.918   68.810   65.833

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     277    277  100.00                60
SUMMARY(RMSD_GDC):     2.708          2.575                  3.656           38.831   34.804

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   60    4.0     33    2.35    43.750    46.728     1.348

LGA_LOCAL      RMSD:   2.349  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.733  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   2.708  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.807300 * X  +  -0.577636 * Y  +  -0.120849 * Z  + -28.906775
  Y_new =   0.241855 * X  +   0.137048 * Y  +   0.960585 * Z  + -142.508865
  Z_new =  -0.538306 * X  +  -0.804708 * Y  +   0.250343 * Z  + 185.294418 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.291077  0.568426 -1.269189   [DEG:   16.6775   32.5684  -72.7192 ]
ZXZ: -3.016442  1.317762 -2.552014   [DEG: -172.8294   75.5022 -146.2196 ]
 
# END of job
