
#######################################################
#                                                     #
#                        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   42 (  353),  selected   42 , name one
# Molecule2: number of CA atoms  108 (  908),  selected   42 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42      58_C - 99_C        4.84     4.84
  LCS_AVERAGE:     38.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      80_C - 99_C        1.63     7.58
  LCS_AVERAGE:     14.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      81_C - 99_C        0.52     7.55
  LCS_AVERAGE:     12.96

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   42
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     K    58_C     K    58_C     14   15   42     13   13   13   14   15   16   16   18   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     I    59_C     I    59_C     14   15   42     13   13   13   14   15   16   16   17   29   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    60_C     L    60_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    61_C     E    61_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     I    62_C     I    62_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     A    63_C     A    63_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    64_C     E    64_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     K    65_C     K    65_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    66_C     L    66_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    67_C     E    67_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     K    68_C     K    68_C     14   15   42     13   13   13   14   15   16   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     A    69_C     A    69_C     14   15   42     13   13   13   14   15   16   17   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    70_C     L    70_C     14   15   42     13   13   13   14   15   16   17   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     P    71_C     P    71_C     14   15   42      3    3    3   14   15   16   17   22   29   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    72_C     E    72_C      4   15   42      4    4    4    5    6    8   12   17   18   19   19   22   31   36   39   40   41   41   42   42 
LCS_GDT     K    73_C     K    73_C      4    5   42      4    4    4    5    5    5    8   12   16   19   19   19   20   23   32   38   39   40   42   42 
LCS_GDT     S    74_C     S    74_C      4    5   42      4    4    4    5    5    5   11   17   18   19   19   22   27   35   39   40   41   41   42   42 
LCS_GDT     K    75_C     K    75_C      4    5   42      4    4    4    6   11   16   16   17   18   20   32   35   37   38   39   40   41   41   42   42 
LCS_GDT     M    76_C     M    76_C      3    5   42      0    3    3    7   13   16   16   17   18   20   31   35   37   38   39   40   41   41   42   42 
LCS_GDT     F    77_C     F    77_C      3    3   42      1    3    4   11   15   15   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     T    78_C     T    78_C      3    3   42      3    4    6    8   12   14   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     K    79_C     K    79_C      3    4   42      3    6    6    8   12   14   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    80_C     E    80_C      3   20   42      3    6    6    6    6    7    7   13   19   23   25   31   37   37   39   40   41   41   42   42 
LCS_GDT     E    81_C     E    81_C     19   20   42     13   18   19   19   19   19   19   20   22   32   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     Y    82_C     Y    82_C     19   20   42     13   18   19   19   19   19   19   20   29   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    83_C     E    83_C     19   20   42     13   18   19   19   19   19   19   22   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     K    84_C     K    84_C     19   20   42     13   18   19   19   19   19   19   22   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    85_C     L    85_C     19   20   42     13   18   19   19   19   19   19   22   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     M    86_C     M    86_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    87_C     E    87_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     V    88_C     V    88_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    89_C     L    89_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    90_C     E    90_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    91_C     E    91_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    92_C     L    92_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    93_C     E    93_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    94_C     E    94_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     V    95_C     V    95_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     L    96_C     L    96_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    97_C     E    97_C     19   20   42     13   18   19   19   19   19   19   26   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     E    98_C     E    98_C     19   20   42     11   18   19   19   19   19   19   21   30   34   35   36   37   38   39   40   41   41   42   42 
LCS_GDT     K    99_C     K    99_C     19   20   42      9   17   19   19   19   19   19   20   20   21   35   36   37   38   39   40   41   41   42   42 
LCS_AVERAGE  LCS_A:  22.10  (  12.96   14.44   38.89 )

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     19     19     19     19     19     26     30     34     35     36     37     38     39     40     41     41     42     42 
GDT PERCENT_AT  12.04  16.67  17.59  17.59  17.59  17.59  17.59  24.07  27.78  31.48  32.41  33.33  34.26  35.19  36.11  37.04  37.96  37.96  38.89  38.89
GDT RMS_LOCAL    0.29   0.47   0.52   0.52   0.52   0.52   0.52   3.09   3.41   3.63   3.71   3.79   3.90   4.10   4.23   4.48   4.61   4.61   4.84   4.84
GDT RMS_ALL_AT   7.14   7.45   7.55   7.55   7.55   7.55   7.55   5.28   5.09   5.01   5.00   4.99   5.06   4.88   4.91   4.84   4.85   4.85   4.84   4.84

# Checking swapping
#   possible swapping detected:  E    64_C      E    64_C
#   possible swapping detected:  E    67_C      E    67_C
#   possible swapping detected:  F    77_C      F    77_C
#   possible swapping detected:  E    80_C      E    80_C
#   possible swapping detected:  E    87_C      E    87_C
#   possible swapping detected:  E    90_C      E    90_C
#   possible swapping detected:  E    91_C      E    91_C
#   possible swapping detected:  E    93_C      E    93_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    58_C      K    58_C     5.024     0    0.107   1.182     8.699   28.810   17.619
LGA    I    59_C      I    59_C     5.201     0    0.029   0.656     8.989   30.238   22.976
LGA    L    60_C      L    60_C     3.847     0    0.089   0.109     4.739   46.905   42.083
LGA    E    61_C      E    61_C     3.144     0    0.015   0.966     7.273   50.119   38.360
LGA    I    62_C      I    62_C     3.854     0    0.062   0.217     6.347   46.667   37.262
LGA    A    63_C      A    63_C     2.977     0    0.057   0.059     3.349   59.167   57.333
LGA    E    64_C      E    64_C     1.713     0    0.038   0.689     2.736   70.833   67.566
LGA    K    65_C      K    65_C     2.638     0    0.029   0.050     4.846   59.048   49.101
LGA    L    66_C      L    66_C     3.024     0    0.039   1.353     7.003   55.357   44.524
LGA    E    67_C      E    67_C     1.670     0    0.208   0.666     2.876   68.810   69.418
LGA    K    68_C      K    68_C     2.142     0    0.066   1.294     7.797   61.190   48.466
LGA    A    69_C      A    69_C     3.851     0    0.148   0.169     4.200   43.452   42.190
LGA    L    70_C      L    70_C     3.951     0    0.628   0.560     4.866   38.810   40.298
LGA    P    71_C      P    71_C     4.519     0    0.533   0.702     7.024   25.714   21.633
LGA    E    72_C      E    72_C    10.876     0    0.593   0.560    14.601    0.714    0.317
LGA    K    73_C      K    73_C    12.358     0    0.073   0.985    14.329    0.000    0.000
LGA    S    74_C      S    74_C    10.515     0    0.144   0.138    11.530    0.476    0.317
LGA    K    75_C      K    75_C     8.886     0    0.613   0.805     9.433    2.976    4.550
LGA    M    76_C      M    76_C     9.142     0    0.613   1.168    15.010    6.310    3.155
LGA    F    77_C      F    77_C     3.258     0    0.592   1.307     4.919   56.786   57.403
LGA    T    78_C      T    78_C     2.014     0    0.632   1.392     4.561   59.881   56.122
LGA    K    79_C      K    79_C     2.468     0    0.252   0.815     8.158   51.786   37.513
LGA    E    80_C      E    80_C     7.163     0    0.221   1.057    13.973   13.571    6.190
LGA    E    81_C      E    81_C     7.342     0    0.553   1.054    10.728   13.452    6.931
LGA    Y    82_C      Y    82_C     6.328     0    0.056   1.336     6.778   18.333   23.413
LGA    E    83_C      E    83_C     5.618     0    0.094   0.152     6.382   25.119   22.593
LGA    K    84_C      K    84_C     5.412     0    0.032   1.146     8.646   26.310   16.772
LGA    L    85_C      L    85_C     5.129     0    0.039   1.220     8.070   30.238   24.464
LGA    M    86_C      M    86_C     4.069     0    0.035   0.811     6.149   41.905   35.655
LGA    E    87_C      E    87_C     3.853     0    0.011   0.872     7.398   43.452   29.418
LGA    V    88_C      V    88_C     3.989     0    0.016   0.090     4.635   43.452   38.299
LGA    L    89_C      L    89_C     3.210     0    0.021   0.163     4.589   53.810   46.369
LGA    E    90_C      E    90_C     1.699     0    0.040   0.930     4.982   72.976   57.989
LGA    E    91_C      E    91_C     2.158     0    0.022   0.581     5.425   64.881   47.407
LGA    L    92_C      L    92_C     3.068     0    0.026   1.409     7.515   55.357   42.024
LGA    E    93_C      E    93_C     1.578     0    0.066   0.585     2.107   70.833   77.778
LGA    E    94_C      E    94_C     1.925     0    0.013   0.825     3.819   65.357   64.550
LGA    V    95_C      V    95_C     3.942     0    0.022   0.133     5.164   40.476   36.667
LGA    L    96_C      L    96_C     3.734     0    0.032   0.070     4.888   41.786   41.905
LGA    E    97_C      E    97_C     3.513     0    0.038   0.242     4.740   40.476   50.635
LGA    E    98_C      E    98_C     5.260     0    0.111   0.157     7.022   22.619   30.741
LGA    K    99_C      K    99_C     6.706     0    0.577   1.224    10.501   14.524    9.630

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       42     168    168  100.00     353    353  100.00               108
SUMMARY(RMSD_GDC):     4.838          4.711                  5.653           15.398   13.589

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42  108    4.0     26    3.09    23.843    21.572     0.814

LGA_LOCAL      RMSD:   3.092  Number of atoms:   26  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.279  Number of assigned atoms:   42 
Std_ASGN_ATOMS RMSD:   4.838  Standard rmsd on all 42 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.959691 * X  +  -0.167737 * Y  +  -0.225516 * Z  +  11.238269
  Y_new =   0.188576 * X  +   0.979257 * Y  +   0.074127 * Z  +   0.115422
  Z_new =   0.208404 * X  +  -0.113666 * Y  +   0.971415 * Z  + -10.276414 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.194025 -0.209943 -0.116481   [DEG:   11.1168  -12.0288   -6.6739 ]
ZXZ: -1.888373  0.239674  2.070112   [DEG: -108.1958   13.7323  118.6087 ]
 
# END of job
