
#######################################################
#                                                     #
#                        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   59 (  471),  selected   59 , name one
# Molecule2: number of CA atoms  126 (  936),  selected   59 , 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:    42      81_A - 122_A       4.88    11.08
  LONGEST_CONTINUOUS_SEGMENT:    42      82_A - 123_A       4.79    11.04
  LCS_AVERAGE:     29.47

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16     103_A - 118_A       1.88    10.91
  LCS_AVERAGE:      9.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13     127_A - 139_A       0.88    22.53
  LCS_AVERAGE:      6.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   59
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     R    81_A     R    81_A      3   12   42      0    3    4    9   10   13   15   16   18   18   19   20   20   21   23   25   27   29   35   39 
LCS_GDT     Y    82_A     Y    82_A     11   12   42      6   10   10   11   12   13   16   21   28   30   32   35   36   38   40   42   43   46   48   49 
LCS_GDT     T    83_A     T    83_A     11   12   42      8   10   10   11   15   19   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     S    84_A     S    84_A     11   12   42      8   10   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     P    85_A     P    85_A     11   12   42      8   10   10   11   12   18   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     E    86_A     E    86_A     11   12   42      8   10   10   11   13   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     A    87_A     A    87_A     11   12   42      8   10   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     L    88_A     L    88_A     11   12   42      8   10   10   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     E    89_A     E    89_A     11   12   42      8   10   10   11   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     R    90_A     R    90_A     11   12   42      8   10   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     S    91_A     S    91_A     11   12   42      6   10   10   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     I    92_A     I    92_A     11   12   42      3    4    6   11   12   19   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     T    93_A     T    93_A      4   12   42      3    4    6    6    7   11   18   21   28   30   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     A    94_A     A    94_A      4    5   42      3    4    6    9   14   19   20   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     L    95_A     L    95_A      4    7   42      3    4    6    6    7   17   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     A    96_A     A    96_A      4    7   42      3    4    4    5    6   12   15   17   21   30   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     A    97_A     A    97_A      5    7   42      3    5    8   11   12   18   23   26   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     M    98_A     M    98_A      5    7   42      3    5    5    6   12   13   14   18   22   27   31   33   36   38   40   42   43   45   47   49 
LCS_GDT     T    99_A     T    99_A      5    7   42      3    5    6    6    7   11   13   18   22   28   31   33   36   38   40   42   43   46   48   49 
LCS_GDT     G   100_A     G   100_A      5    7   42      3    5    6    6    7    9   12   17   22   25   28   33   36   38   40   42   43   45   47   49 
LCS_GDT     H   101_A     H   101_A      5    7   42      3    5    6    6    7    9   12   17   22   25   29   33   36   38   40   42   43   46   48   49 
LCS_GDT     A   102_A     A   102_A      4    7   42      3    5    5    6    6    8   14   22   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     P   103_A     P   103_A      6   16   42      5    6    6   10   16   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     S   104_A     S   104_A      6   16   42      5    6    7   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     S   105_A     S   105_A      6   16   42      5    6    6   10   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     I   106_A     I   106_A      6   16   42      5    6    6    9   16   19   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     K   107_A     K   107_A      6   16   42      5    6    6   10   16   19   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     E   108_A     E   108_A      6   16   42      4    6    7   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     E   109_A     E   109_A     10   16   42      7    9   12   12   16   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     C   110_A     C   110_A     10   16   42      7    9   12   12   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     V   111_A     V   111_A     10   16   42      7    9   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     E   112_A     E   112_A     10   16   42      7    9   12   12   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     L   113_A     L   113_A     10   16   42      7    9   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     I   114_A     I   114_A     10   16   42      7    9   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     D   115_A     D   115_A     10   16   42      7    9   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     K   116_A     K   116_A     10   16   42      6    9   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     L   117_A     L   117_A     10   16   42      6    9   12   13   17   20   24   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     D   118_A     D   118_A     10   16   42      3    3    3   10   16   17   23   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     W   119_A     W   119_A      3    3   42      3    3    3    5    8   18   22   27   30   31   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     L   120_A     L   120_A      3    5   42      3    3    3    3    5    9   15   17   21   26   27   34   36   38   40   42   43   46   48   49 
LCS_GDT     R   121_A     R   121_A      3    5   42      3    3    3    3    5    5   10   16   24   30   33   35   36   38   40   42   43   46   48   49 
LCS_GDT     V   122_A     V   122_A      3    5   42      3    3    4    5    6   10   13   15   18   18   21   27   35   38   40   41   43   46   48   49 
LCS_GDT     E   123_A     E   123_A      3    5   42      3    3    4    5    7   10   13   15   18   18   19   20   23   29   31   32   41   43   48   49 
LCS_GDT     N   124_A     N   124_A      3   10   28      3    3    3    5    7   10   13   16   18   19   22   25   26   31   35   40   42   43   48   49 
LCS_GDT     D   125_A     D   125_A      8   15   28      3    5    8    9   11   12   14   15   16   17   19   19   22   27   31   31   33   36   43   43 
LCS_GDT     V   126_A     V   126_A      8   15   28      3    5    8   10   12   14   15   16   17   19   22   25   26   31   35   40   42   44   48   49 
LCS_GDT     I   127_A     I   127_A     13   15   28      3    5   10   13   13   14   15   16   18   18   22   25   26   29   34   40   42   46   48   49 
LCS_GDT     Q   128_A     Q   128_A     13   15   28      5   12   12   13   13   14   15   16   19   20   23   28   34   38   40   42   43   46   48   49 
LCS_GDT     Y   129_A     Y   129_A     13   15   28      6   12   12   13   13   14   15   16   19   20   22   28   33   37   40   42   43   46   48   49 
LCS_GDT     P   130_A     P   130_A     13   15   28      5   12   12   13   13   14   15   16   18   18   20   25   26   30   33   41   43   46   48   49 
LCS_GDT     T   131_A     T   131_A     13   15   21      7   12   12   13   13   14   15   16   18   18   19   20   23   29   31   36   43   46   48   49 
LCS_GDT     L   132_A     L   132_A     13   15   21      7   12   12   13   13   14   15   16   18   18   19   20   22   29   31   36   43   46   48   49 
LCS_GDT     S   133_A     S   133_A     13   15   21      7   12   12   13   13   14   15   16   18   18   20   23   26   29   31   36   43   46   48   49 
LCS_GDT     K   134_A     K   134_A     13   15   21      7   12   12   13   13   14   15   16   18   18   19   20   20   23   24   28   30   31   36   40 
LCS_GDT     L   135_A     L   135_A     13   15   21      7   12   12   13   13   14   15   16   18   18   19   20   20   23   24   28   28   28   32   36 
LCS_GDT     L   136_A     L   136_A     13   15   21      7   12   12   13   13   14   15   16   18   18   19   20   20   23   24   28   28   30   34   37 
LCS_GDT     E   137_A     E   137_A     13   15   21      7   12   12   13   13   14   15   16   18   18   19   20   20   23   24   28   28   30   33   37 
LCS_GDT     L   138_A     L   138_A     13   15   21      6   12   12   13   13   14   15   16   18   18   19   20   20   23   23   28   28   28   29   34 
LCS_GDT     Y   139_A     Y   139_A     13   15   21      6   12   12   13   13   14   15   16   18   18   19   20   20   23   23   28   28   28   29   33 
LCS_AVERAGE  LCS_A:  15.38  (   6.83    9.83   29.47 )

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      8     12     12     13     17     20     24     27     30     31     33     35     36     38     40     42     43     46     48     49 
GDT PERCENT_AT   6.35   9.52   9.52  10.32  13.49  15.87  19.05  21.43  23.81  24.60  26.19  27.78  28.57  30.16  31.75  33.33  34.13  36.51  38.10  38.89
GDT RMS_LOCAL    0.20   0.55   0.55   0.88   1.89   2.10   2.44   2.61   2.90   3.02   3.23   3.53   3.81   4.04   4.33   4.82   5.21   6.07   6.36   6.33
GDT RMS_ALL_AT  14.49  22.90  22.90  22.53  11.45  11.47  11.42  11.34  11.36  11.41  11.46  11.21  11.16  11.04  11.05  10.62  10.36   9.80   9.76   9.83

# Checking swapping
#   possible swapping detected:  Y    82_A      Y    82_A
#   possible swapping detected:  E    89_A      E    89_A
#   possible swapping detected:  D   118_A      D   118_A
#   possible swapping detected:  D   125_A      D   125_A
#   possible swapping detected:  Y   129_A      Y   129_A
#   possible swapping detected:  Y   139_A      Y   139_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    81_A      R    81_A    12.707     0    0.118   1.334    22.881    0.000    0.000
LGA    Y    82_A      Y    82_A     5.393     0    0.720   1.199     7.876   28.452   26.786
LGA    T    83_A      T    83_A     3.075     0    0.014   0.139     4.364   50.119   49.388
LGA    S    84_A      S    84_A     1.998     0    0.039   0.050     2.467   68.810   67.460
LGA    P    85_A      P    85_A     3.679     0    0.100   0.164     4.926   48.333   41.905
LGA    E    86_A      E    86_A     3.368     0    0.067   0.897     4.983   55.476   44.074
LGA    A    87_A      A    87_A     1.831     0    0.060   0.063     2.123   72.976   72.952
LGA    L    88_A      L    88_A     1.934     0    0.047   0.054     4.531   72.857   59.167
LGA    E    89_A      E    89_A     2.417     0    0.043   1.090     3.314   70.833   63.333
LGA    R    90_A      R    90_A     2.370     0    0.046   1.436     3.824   66.786   65.152
LGA    S    91_A      S    91_A     2.154     0    0.569   0.711     2.797   68.810   64.921
LGA    I    92_A      I    92_A     3.570     0    0.243   1.558    10.380   45.000   29.048
LGA    T    93_A      T    93_A     6.311     0    0.575   1.296     9.360   21.786   13.741
LGA    A    94_A      A    94_A     4.996     0    0.364   0.371     6.299   34.881   31.333
LGA    L    95_A      L    95_A     3.643     0    0.547   0.633     6.578   38.333   31.964
LGA    A    96_A      A    96_A     6.609     0    0.595   0.605     7.811   21.786   18.857
LGA    A    97_A      A    97_A     5.813     0    0.060   0.055     8.575   15.119   16.381
LGA    M    98_A      M    98_A     9.608     0    0.061   0.164    14.364    2.024    1.012
LGA    T    99_A      T    99_A     9.212     0    0.580   0.474    10.577    1.190    3.469
LGA    G   100_A      G   100_A    10.675     0    0.097   0.097    11.854    0.119    0.119
LGA    H   101_A      H   101_A     8.766     5    0.065   0.101     9.297   14.643    6.000
LGA    A   102_A      A   102_A     5.478     0    0.096   0.116     7.668   34.881   29.333
LGA    P   103_A      P   103_A     2.606     0    0.601   0.601     5.225   60.952   48.503
LGA    S   104_A      S   104_A     1.471     0    0.043   0.173     1.711   77.143   78.571
LGA    S   105_A      S   105_A     2.219     0    0.067   0.655     3.579   59.524   57.540
LGA    I   106_A      I   106_A     3.470     0    0.058   1.117     6.190   48.452   51.071
LGA    K   107_A      K   107_A     3.321     0    0.370   0.742     6.195   57.381   40.635
LGA    E   108_A      E   108_A     1.616     3    0.045   0.709     3.242   66.905   43.386
LGA    E   109_A      E   109_A     3.353     0    0.261   0.458     7.544   53.690   35.450
LGA    C   110_A      C   110_A     2.534     0    0.053   0.754     3.461   62.976   59.841
LGA    V   111_A      V   111_A     2.080     0    0.032   0.141     2.649   66.786   64.830
LGA    E   112_A      E   112_A     2.911     0    0.032   0.400     7.124   60.952   41.799
LGA    L   113_A      L   113_A     1.748     0    0.039   0.103     3.419   75.119   66.190
LGA    I   114_A      I   114_A     1.267     0    0.109   0.109     2.297   81.429   77.262
LGA    D   115_A      D   115_A     1.829     0    0.126   1.020     3.761   72.976   62.560
LGA    K   116_A      K   116_A     0.808     2    0.034   0.171     1.400   85.952   66.349
LGA    L   117_A      L   117_A     1.568     0    0.578   0.633     3.829   65.595   67.262
LGA    D   118_A      D   118_A     3.858     0    0.546   0.948     8.775   55.833   31.429
LGA    W   119_A      W   119_A     4.872     0    0.616   0.906     8.068   29.524   25.340
LGA    L   120_A      L   120_A     9.173     0    0.639   1.492    14.776    4.048    2.024
LGA    R   121_A      R   121_A     7.901     0    0.609   1.154    12.674    8.095    4.416
LGA    V   122_A      V   122_A     9.004     0    0.533   0.895     9.877    1.548    1.224
LGA    E   123_A      E   123_A    11.971     4    0.589   0.631    12.566    0.000    0.000
LGA    N   124_A      N   124_A    10.955     0    0.128   0.869    15.564    0.000    0.000
LGA    D   125_A      D   125_A    13.266     0    0.496   1.302    14.587    0.000    0.000
LGA    V   126_A      V   126_A    10.748     0    0.047   1.109    11.276    0.000    0.476
LGA    I   127_A      I   127_A    11.379     0    0.074   1.043    16.232    0.119    0.060
LGA    Q   128_A      Q   128_A    11.174     0    0.075   1.238    14.172    0.000    0.000
LGA    Y   129_A      Y   129_A    12.727     0    0.017   1.381    15.030    0.000    0.000
LGA    P   130_A      P   130_A    17.603     0    0.046   0.122    19.113    0.000    0.000
LGA    T   131_A      T   131_A    16.516     0    0.051   0.117    18.208    0.000    0.000
LGA    L   132_A      L   132_A    14.725     0    0.041   1.401    17.447    0.000    0.000
LGA    S   133_A      S   133_A    18.122     0    0.040   0.103    21.768    0.000    0.000
LGA    K   134_A      K   134_A    23.505     4    0.055   0.060    26.153    0.000    0.000
LGA    L   135_A      L   135_A    23.226     0    0.066   0.326    25.670    0.000    0.000
LGA    L   136_A      L   136_A    22.452     0    0.082   0.429    25.940    0.000    0.000
LGA    E   137_A      E   137_A    27.519     4    0.092   0.086    31.261    0.000    0.000
LGA    L   138_A      L   138_A    31.328     3    0.052   0.060    34.454    0.000    0.000
LGA    Y   139_A      Y   139_A    31.455     0    0.619   1.284    32.878    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       59     236    236  100.00     446    446  100.00               126
SUMMARY(RMSD_GDC):     9.135          9.184                  9.742           15.303   13.195

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   59  126    4.0     27    2.61    18.651    16.845     0.997

LGA_LOCAL      RMSD:   2.607  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.341  Number of assigned atoms:   59 
Std_ASGN_ATOMS RMSD:   9.135  Standard rmsd on all 59 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.031984 * X  +   0.998438 * Y  +   0.045812 * Z  + -45.991066
  Y_new =  -0.125696 * X  +   0.049489 * Y  +  -0.990834 * Z  + 105.652130
  Z_new =  -0.991553 * X  +   0.025933 * Y  +   0.127082 * Z  +  47.394470 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.321627  1.440729  0.201299   [DEG:  -75.7236   82.5477   11.5336 ]
ZXZ:  0.046203  1.443370 -1.544649   [DEG:    2.6472   82.6990  -88.5019 ]
 
# END of job
