
#######################################################
#                                                     #
#                        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        2.42     2.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       1_A - 29_A        1.99     3.54
  LCS_AVERAGE:     68.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       1_A - 20_A        0.80     5.20
  LCS_AVERAGE:     48.65

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     20   29   39      5   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     20   29   39      6   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     20   29   39     12   17   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     20   29   39     12   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     20   29   39     12   18   21   22   28   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     20   29   39     11   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     20   29   39      9   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     20   29   39      5   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     20   29   39      9   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     20   29   39      6   18   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     20   29   39      3   13   21   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     18   29   39      6   15   17   20   25   31   34   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     18   29   39      5   15   17   22   28   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     18   29   39      5   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     18   29   39      5   14   17   19   22   28   33   36   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     18   29   39      5   14   17   20   22   30   34   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     18   29   39      7   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     18   29   39      7   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     18   29   39      8   15   21   22   28   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     18   29   39      8   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     18   20   39      8   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     18   20   39      8   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     18   20   39      8   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     18   20   39      8   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     18   20   39      8   15   17   22   27   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     18   20   39      8   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     18   20   39      7   15   17   22   29   33   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     18   20   39      7   15   17   20   25   32   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     18   20   39      3    7   17   20   25   31   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     16   20   39      0    3    3    3   24   32   36   38   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  72.36  (  48.65   68.44  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     12     18     21     22     29     33     36     38     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  30.77  46.15  53.85  56.41  74.36  84.62  92.31  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    0.24   0.63   0.88   1.23   1.78   1.96   2.15   2.34   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42
GDT RMS_ALL_AT   5.24   5.22   4.81   3.80   2.64   2.57   2.48   2.43   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  D    17_A      D    17_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  D    30_A      D    30_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     2.988     0    0.134   1.101     5.667   53.690   45.238
LGA    K     2_A      K     2_A     2.954     0    0.089   0.715     5.595   55.357   47.143
LGA    L     3_A      L     3_A     2.166     0    0.021   0.074     2.937   69.048   66.964
LGA    W     4_A      W     4_A     1.767     0    0.096   1.113     6.452   75.000   46.769
LGA    I     5_A      I     5_A     2.655     0    0.088   1.391     6.538   64.881   50.357
LGA    L     6_A      L     6_A     2.142     0    0.050   1.380     3.732   73.095   67.381
LGA    Q     7_A      Q     7_A     0.619     0    0.043   1.509     5.859   92.857   70.106
LGA    K     8_A      K     8_A     1.310     0    0.047   0.881     9.081   88.214   57.196
LGA    I     9_A      I     9_A     1.354     0    0.061   0.095     3.896   83.690   69.643
LGA    Y    10_A      Y    10_A     2.005     0    0.034   0.087     6.338   70.952   47.698
LGA    E    11_A      E    11_A     2.090     0    0.038   0.049     3.955   68.810   56.931
LGA    I    12_A      I    12_A     0.948     0    0.053   0.794     3.504   88.214   77.976
LGA    M    13_A      M    13_A     1.468     0    0.038   0.107     3.783   79.405   66.607
LGA    V    14_A      V    14_A     3.172     0    0.057   0.050     4.818   53.690   46.667
LGA    R    15_A      R    15_A     3.048     0    0.043   1.102     8.225   57.262   34.935
LGA    L    16_A      L    16_A     0.407     0    0.062   0.133     1.532   92.976   87.262
LGA    D    17_A      D    17_A     2.100     0    0.072   0.955     3.548   68.929   58.631
LGA    E    18_A      E    18_A     3.628     0    0.076   0.173     7.142   48.452   32.434
LGA    E    19_A      E    19_A     2.950     0    0.294   0.359     6.220   62.976   44.762
LGA    G    20_A      G    20_A     1.379     0    0.723   0.723     3.931   67.619   67.619
LGA    H    21_A      H    21_A     4.436     0    0.506   0.764     9.441   43.690   20.714
LGA    G    22_A      G    22_A     2.282     0    0.108   0.108     2.691   66.905   66.905
LGA    E    23_A      E    23_A     1.946     0    0.042   0.327     7.911   69.048   44.339
LGA    A    24_A      A    24_A     4.615     0    0.091   0.094     6.040   37.262   33.238
LGA    S    25_A      S    25_A     4.111     0    0.047   0.574     5.094   45.119   39.683
LGA    L    26_A      L    26_A     1.246     0    0.069   0.074     3.267   83.810   74.524
LGA    M    27_A      M    27_A     2.060     0    0.061   1.069     6.323   70.952   51.071
LGA    V    28_A      V    28_A     2.877     0    0.065   0.135     4.702   62.857   51.088
LGA    S    29_A      S    29_A     1.967     0    0.027   0.578     2.399   77.143   73.016
LGA    D    30_A      D    30_A     1.069     0    0.051   0.180     1.637   83.690   79.345
LGA    L    31_A      L    31_A     1.438     0    0.031   1.415     5.397   81.429   69.405
LGA    I    32_A      I    32_A     1.053     0    0.039   0.115     3.060   83.690   73.393
LGA    Y    33_A      Y    33_A     1.765     0    0.053   0.111     4.298   72.976   57.897
LGA    E    34_A      E    34_A     2.319     0    0.035   0.245     5.596   68.810   51.058
LGA    F    35_A      F    35_A     1.247     0    0.056   0.640     6.168   85.952   57.879
LGA    M    36_A      M    36_A     1.554     0    0.133   0.125     4.731   71.310   60.238
LGA    K    37_A      K    37_A     3.028     0    0.164   0.965    10.725   52.024   33.228
LGA    R    38_A      R    38_A     3.333     0    0.589   1.120     7.419   47.143   36.623
LGA    D    39_A      D    39_A     2.801     3    0.193   0.278     4.933   59.286   33.571

# 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):     2.422          2.291                  3.676           68.672   55.116

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     38    2.34    75.000    78.154     1.556

LGA_LOCAL      RMSD:   2.343  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.428  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   2.422  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.242433 * X  +  -0.578554 * Y  +  -0.778782 * Z  +  -1.725686
  Y_new =  -0.896293 * X  +   0.440806 * Y  +  -0.048459 * Z  + -26.221924
  Z_new =   0.371328 * X  +   0.686269 * Y  +  -0.625420 * Z  +  12.034894 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.834959 -0.380439  2.309838   [DEG: -105.1354  -21.7976  132.3439 ]
ZXZ: -1.508652  2.246466  0.495971   [DEG:  -86.4394  128.7130   28.4170 ]
 
# END of job
