
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   39 (  326),  selected   39 , 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:    39       1_A - 39_A        1.66     1.66
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        1.66     1.66
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       1_A - 19_A        0.92     2.43
  LONGEST_CONTINUOUS_SEGMENT:    19       3_A - 21_A        0.99     2.42
  LCS_AVERAGE:     47.34

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     D     1_A     D     1_A     19   39   39      3   16   23   34   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     19   39   39     13   17   23   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     19   39   39     13   17   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     19   39   39     13   17   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     19   39   39     13   17   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     19   39   39     13   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     19   39   39      8   17   26   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     19   39   39      8   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     19   39   39     10   17   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     19   39   39      5   14   24   34   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     19   39   39      5   16   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     19   39   39     10   16   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     19   39   39      3    9   19   27   36   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     19   39   39      7   17   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     18   39   39      4   16   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     18   39   39     10   17   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     18   39   39     10   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     18   39   39      8   18   27   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     18   39   39      8   18   26   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     18   39   39      8   17   25   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     18   39   39     13   17   25   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     18   39   39      8   17   25   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     18   39   39      3   17   25   35   37   38   38   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     15   39   39      0    3    3    3   15   24   29   37   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  82.45  (  47.34  100.00  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     13     18     27     35     37     38     38     38     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  33.33  46.15  69.23  89.74  94.87  97.44  97.44  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.66   1.02   1.30   1.36   1.45   1.45   1.45   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66
GDT RMS_ALL_AT   2.46   1.91   1.92   1.68   1.68   1.68   1.68   1.68   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    34_A      E    34_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     2.029     0    0.669   1.227     7.242   61.429   41.726
LGA    K     2_A      K     2_A     1.823     0    0.073   1.361     5.778   75.000   63.228
LGA    L     3_A      L     3_A     1.010     0    0.075   1.067     2.724   83.690   79.702
LGA    W     4_A      W     4_A     1.355     0    0.047   1.292     8.341   81.429   44.456
LGA    I     5_A      I     5_A     1.566     0    0.050   0.602     4.354   79.405   68.631
LGA    L     6_A      L     6_A     0.697     0    0.034   0.103     1.915   92.857   86.131
LGA    Q     7_A      Q     7_A     0.885     0    0.024   0.292     2.127   88.214   79.735
LGA    K     8_A      K     8_A     1.314     0    0.096   0.749     7.419   85.952   57.619
LGA    I     9_A      I     9_A     0.512     0    0.046   1.260     3.722   90.476   78.214
LGA    Y    10_A      Y    10_A     0.845     0    0.038   0.050     2.246   88.214   79.444
LGA    E    11_A      E    11_A     1.270     0    0.053   1.047     2.530   81.429   77.831
LGA    I    12_A      I    12_A     0.681     0    0.035   0.636     1.844   90.476   89.464
LGA    M    13_A      M    13_A     0.835     0    0.040   0.869     2.874   85.952   84.048
LGA    V    14_A      V    14_A     1.395     0    0.037   1.251     4.613   81.429   69.592
LGA    R    15_A      R    15_A     0.820     0    0.059   1.229     5.906   95.238   67.706
LGA    L    16_A      L    16_A     1.088     0    0.046   1.176     3.432   81.548   76.488
LGA    D    17_A      D    17_A     1.940     0    0.034   0.125     3.174   72.976   65.119
LGA    E    18_A      E    18_A     1.089     0    0.080   0.865     4.867   79.286   67.037
LGA    E    19_A      E    19_A     1.750     0    0.276   1.027     4.993   63.690   52.063
LGA    G    20_A      G    20_A     3.208     0    0.062   0.062     3.439   55.476   55.476
LGA    H    21_A      H    21_A     1.534     0    0.181   0.808     3.726   79.405   65.619
LGA    G    22_A      G    22_A     1.549     0    0.025   0.025     1.549   77.143   77.143
LGA    E    23_A      E    23_A     1.531     0    0.048   0.326     5.818   79.286   58.624
LGA    A    24_A      A    24_A     0.979     0    0.041   0.038     1.185   90.476   88.667
LGA    S    25_A      S    25_A     0.490     0    0.034   0.578     3.041   95.238   85.397
LGA    L    26_A      L    26_A     1.805     0    0.045   1.010     4.735   75.000   65.774
LGA    M    27_A      M    27_A     1.849     0    0.047   0.966     2.960   77.143   73.095
LGA    V    28_A      V    28_A     0.776     0    0.039   0.067     1.039   88.214   90.544
LGA    S    29_A      S    29_A     1.042     0    0.078   0.536     3.292   83.690   77.698
LGA    D    30_A      D    30_A     1.641     0    0.047   1.172     6.666   77.143   57.202
LGA    L    31_A      L    31_A     1.233     0    0.020   1.080     3.543   85.952   77.857
LGA    I    32_A      I    32_A     0.547     0    0.038   1.404     3.176   90.476   79.226
LGA    Y    33_A      Y    33_A     0.714     0    0.046   0.220     1.369   90.476   87.460
LGA    E    34_A      E    34_A     1.349     0    0.038   1.077     2.422   79.286   73.016
LGA    F    35_A      F    35_A     2.079     0    0.041   0.476     5.639   66.786   49.221
LGA    M    36_A      M    36_A     1.998     0    0.139   0.642     3.550   72.857   63.333
LGA    K    37_A      K    37_A     1.367     0    0.175   1.278     8.479   75.119   57.196
LGA    R    38_A      R    38_A     2.100     0    0.552   0.769     4.998   70.952   50.952
LGA    D    39_A      D    39_A     5.550     3    0.552   0.578     8.424   20.833   11.012

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     326    326  100.00                39
SUMMARY(RMSD_GDC):     1.665          1.681                  2.731           79.222   68.532

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     38    1.45    83.333    91.959     2.454

LGA_LOCAL      RMSD:   1.448  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.683  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   1.665  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.656626 * X  +   0.253047 * Y  +  -0.710499 * Z  + 164.922836
  Y_new =   0.202758 * X  +   0.966583 * Y  +   0.156868 * Z  + -159.494431
  Z_new =   0.726451 * X  +  -0.041056 * Y  +  -0.685991 * Z  + -20.916967 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.842094 -0.813144 -3.081815   [DEG:  162.8400  -46.5897 -176.5750 ]
ZXZ: -1.788096  2.326761  1.627252   [DEG: -102.4503  133.3136   93.2346 ]
 
# END of job
