
#######################################################
#                                                     #
#                        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   56 (  449),  selected   56 , name one
# Molecule2: number of CA atoms  255 ( 2029),  selected   56 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23     146_B - 168_B       4.98    14.78
  LCS_AVERAGE:      7.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10     185_B - 194_B       1.94    12.66
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6     174_B - 179_B       0.96    21.75
  LONGEST_CONTINUOUS_SEGMENT:     6     175_B - 180_B       0.83    21.72
  LONGEST_CONTINUOUS_SEGMENT:     6     185_B - 190_B       0.86    12.58
  LCS_AVERAGE:      1.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   56
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     L   146_B     L   146_B      4    6   23      3    4    5    9   11   13   14   14   16   16   18   19   21   21   23   24   26   29   30   34 
LCS_GDT     T   147_B     T   147_B      4    6   23      3    4    6    9   11   13   14   14   16   16   18   19   21   21   23   24   26   29   30   32 
LCS_GDT     C   148_B     C   148_B      4    6   23      4    4    6    9   11   13   14   14   16   16   18   19   21   21   23   24   26   29   31   35 
LCS_GDT     L   149_B     L   149_B      4    6   23      4    4    6    9   11   13   14   14   16   16   18   19   21   21   22   24   26   29   30   32 
LCS_GDT     V   150_B     V   150_B      4    6   23      4    4    5    6    8   13   14   14   16   17   18   19   21   21   23   24   26   29   31   35 
LCS_GDT     K   151_B     K   151_B      4    7   23      4    4    5    8   11   13   14   14   16   17   18   19   21   21   23   24   26   29   30   32 
LCS_GDT     G   152_B     G   152_B      3    7   23      0    3    4    6    7   12   13   15   17   17   19   19   21   21   24   24   26   29   32   35 
LCS_GDT     F   153_B     F   153_B      3    7   23      2    3    4    6    7    7   14   14   17   17   19   19   21   22   24   24   26   29   32   35 
LCS_GDT     Y   154_B     Y   154_B      4    7   23      0    4    4    5    7    7   11   14   16   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     P   155_B     P   155_B      4    7   23      3    4    5    5    6    7   10   11   13   15   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     S   156_B     S   156_B      4    7   23      3    4    4    4    6    7   14   15   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     D   157_B     D   157_B      4    7   23      3    4    4    5    8   12   14   14   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     I   158_B     I   158_B      5    8   23      3    5    6    9   11   13   14   15   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     A   159_B     A   159_B      5    8   23      3    5    5    7   11   13   14   15   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     V   160_B     V   160_B      5    8   23      3    5    6    9   11   13   14   15   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     E   161_B     E   161_B      5    8   23      4    5    6    9   11   13   14   15   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     W   162_B     W   162_B      5    8   23      4    5    5    9   11   13   14   15   17   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     E   163_B     E   163_B      5    8   23      4    5    5    7   10   13   14   15   17   17   19   21   22   23   24   24   26   28   32   35 
LCS_GDT     S   164_B     S   164_B      5    8   23      4    5    5    9   11   13   14   15   17   17   19   21   22   23   24   24   26   28   32   35 
LCS_GDT     N   165_B     N   165_B      5    8   23      3    5    5    7   10   12   14   15   17   17   19   21   22   23   24   24   26   28   32   35 
LCS_GDT     G   166_B     G   166_B      4    8   23      3    4    5    6   10   12   14   15   17   17   19   21   22   23   24   24   26   28   32   35 
LCS_GDT     Q   167_B     Q   167_B      4    6   23      3    4    4    4    6    8   11   14   16   17   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     P   168_B     P   168_B      4    7   23      3    4    4    5    6    7    9   10   14   16   19   21   22   23   24   24   26   29   32   35 
LCS_GDT     E   169_B     E   169_B      4    7   19      3    4    4    5    7    8    9   10   10   11   14   18   22   23   24   24   26   29   32   35 
LCS_GDT     N   170_B     N   170_B      4    7   19      3    4    4    5    7    8    9   10   10   14   17   21   22   23   24   24   26   29   32   35 
LCS_GDT     N   171_B     N   171_B      4    7   19      3    4    4    5    6    7    9   10   12   15   18   21   22   23   24   24   26   29   32   35 
LCS_GDT     Y   172_B     Y   172_B      5    9   15      3    4    5    7    8    9    9   10   10   11   12   13   14   18   21   24   26   29   32   35 
LCS_GDT     K   173_B     K   173_B      5    9   15      4    4    6    7    8    9    9   10   10   11   12   13   17   18   21   24   26   29   32   35 
LCS_GDT     T   174_B     T   174_B      6    9   15      4    4    6    7    8    9    9   10   10   11   12   13   14   15   17   19   25   29   30   34 
LCS_GDT     T   175_B     T   175_B      6    9   15      5    5    6    7    8    9    9   10   10   11   12   13   14   17   21   24   26   29   30   35 
LCS_GDT     P   176_B     P   176_B      6    9   15      5    5    6    7    8    9    9   10   10   11   12   13   14   16   21   24   26   27   30   30 
LCS_GDT     P   177_B     P   177_B      6    9   15      5    5    6    7    8    9    9   10   10   11   12   13   14   16   21   24   26   29   30   34 
LCS_GDT     V   178_B     V   178_B      6    9   15      5    5    6    7    8    9    9    9   10   11   12   13   14   16   18   24   26   29   32   35 
LCS_GDT     L   179_B     L   179_B      6    9   15      5    5    6    7    8    9    9    9   10   11   12   13   14   15   17   22   26   29   32   35 
LCS_GDT     D   180_B     D   180_B      6    9   15      3    5    6    7    8    9    9    9   10   11   11   13   14   16   18   20   22   28   32   35 
LCS_GDT     S   181_B     S   181_B      4    6   15      3    4    5    5    6    7    7    8    8    9   11   13   13   14   16   17   18   20   21   23 
LCS_GDT     D   182_B     D   182_B      4    6   15      3    4    5    5    6    7    7    9   10   11   11   13   14   16   18   20   20   21   22   23 
LCS_GDT     G   183_B     G   183_B      4    6   15      3    4    4    5    6    7    7    9   10   11   11   13   14   16   18   20   20   23   26   30 
LCS_GDT     S   184_B     S   184_B      4    8   16      3    3    4    5    7    8    8   11   11   12   14   18   19   20   22   24   25   26   29   34 
LCS_GDT     F   185_B     F   185_B      6   10   16      3    3    6    7    8   10   13   14   16   17   19   19   20   21   22   24   25   28   32   35 
LCS_GDT     F   186_B     F   186_B      6   10   16      4    5    6    7   10   11   13   14   16   17   19   19   20   23   23   24   25   28   32   35 
LCS_GDT     L   187_B     L   187_B      6   10   16      4    5    6    7   10   11   13   14   16   17   19   21   22   23   23   24   25   28   32   35 
LCS_GDT     Y   188_B     Y   188_B      6   10   16      4    5    6    7   10   11   13   14   16   17   19   21   22   23   23   24   25   28   32   35 
LCS_GDT     S   189_B     S   189_B      6   10   16      3    5    6    7   10   11   13   14   16   17   19   21   22   23   24   24   26   28   32   35 
LCS_GDT     K   190_B     K   190_B      6   10   16      4    5    6    7   10   11   13   14   16   17   19   21   22   23   24   24   26   28   32   35 
LCS_GDT     L   191_B     L   191_B      5   10   16      3    5    5    7   10   11   14   15   17   17   19   19   20   22   24   24   26   28   31   35 
LCS_GDT     T   192_B     T   192_B      5   10   16      3    5    5    7   10   11   14   15   17   17   19   19   20   22   24   24   26   28   32   35 
LCS_GDT     V   193_B     V   193_B      5   10   16      3    5    5    7    9   12   13   15   17   17   19   19   20   21   22   24   26   28   29   32 
LCS_GDT     D   194_B     D   194_B      5   10   16      3    3    5    7   10   12   13   15   17   17   19   19   20   21   22   24   26   28   30   33 
LCS_GDT     K   195_B     K   195_B      3    5   16      3    3    4    4    6    9   12   14   16   17   19   19   20   21   22   24   26   28   31   35 
LCS_GDT     S   196_B     S   196_B      4    5   16      3    4    4    4    5    6    6   10   11   14   18   19   20   21   22   24   25   26   28   30 
LCS_GDT     R   197_B     R   197_B      4    5   16      3    4    4    4    6    9   11   13   15   17   19   19   20   21   22   24   25   26   27   30 
LCS_GDT     W   198_B     W   198_B      4    5   16      3    4    4    4    6    9   10   13   15   17   19   19   20   21   22   24   25   26   28   30 
LCS_GDT     Q   199_B     Q   199_B      4    5   16      3    4    4    4    6    8    8   10   11   11   14   15   20   21   22   23   24   26   27   29 
LCS_GDT     Q   200_B     Q   200_B      4    5   14      3    3    4    4    6    8    8   10   11   11   12   12   13   14   14   20   20   21   23   23 
LCS_GDT     G   201_B     G   201_B      4    5   14      3    3    4    4    6    8    8   10   11   11   14   14   15   18   19   20   21   21   25   26 
LCS_AVERAGE  LCS_A:   4.06  (   1.83    2.99    7.35 )

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      5      5      6      9     11     13     14     15     17     17     19     21     22     23     24     24     26     29     32     35 
GDT PERCENT_AT   1.96   1.96   2.35   3.53   4.31   5.10   5.49   5.88   6.67   6.67   7.45   8.24   8.63   9.02   9.41   9.41  10.20  11.37  12.55  13.73
GDT RMS_LOCAL    0.37   0.37   0.83   1.30   1.72   2.02   2.21   2.80   3.15   3.15   3.58   4.47   4.61   4.77   5.30   4.95   5.38   6.57   7.30   7.70
GDT RMS_ALL_AT  21.77  21.77  21.72  15.61  15.48  15.55  15.44  13.14  13.30  13.30  13.37  13.28  13.34  13.47  12.34  12.63  13.50  14.88  12.17  11.88

# Checking swapping
#   possible swapping detected:  F   153_B      F   153_B
#   possible swapping detected:  Y   172_B      Y   172_B
#   possible swapping detected:  D   180_B      D   180_B
#   possible swapping detected:  D   182_B      D   182_B
#   possible swapping detected:  F   185_B      F   185_B
#   possible swapping detected:  D   194_B      D   194_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L   146_B      L   146_B    12.939     0    0.034   0.809    13.954    0.000    0.000
LGA    T   147_B      T   147_B    11.632     0    0.103   0.124    13.480    0.000    0.000
LGA    C   148_B      C   148_B     9.271     0    0.233   0.841    10.270    0.595    5.159
LGA    L   149_B      L   149_B    11.263     0    0.055   1.167    15.773    2.500    1.250
LGA    V   150_B      V   150_B     6.071     0    0.076   0.179     8.566    9.524   17.551
LGA    K   151_B      K   151_B     7.361     0    0.570   1.251    15.767   22.976   10.370
LGA    G   152_B      G   152_B     2.748     0    0.565   0.565     4.678   43.929   43.929
LGA    F   153_B      F   153_B     6.095     0    0.569   1.267    10.442   19.405    8.745
LGA    Y   154_B      Y   154_B     8.957     0    0.040   1.234     9.534    3.333    5.238
LGA    P   155_B      P   155_B    10.340     0    0.189   0.411    14.357    4.286    2.449
LGA    S   156_B      S   156_B     4.617     0    0.714   0.591     7.152   29.762   25.873
LGA    D   157_B      D   157_B     5.214     0    0.605   0.628     8.293   27.976   18.512
LGA    I   158_B      I   158_B     2.019     0    0.622   0.637     7.424   77.738   55.893
LGA    A   159_B      A   159_B     2.465     0    0.037   0.041     5.116   67.262   59.048
LGA    V   160_B      V   160_B     2.009     0    0.083   1.168     6.943   63.452   45.714
LGA    E   161_B      E   161_B     2.210     0    0.182   0.763    10.478   71.190   37.513
LGA    W   162_B      W   162_B     2.476     0    0.064   0.568    14.509   59.405   21.054
LGA    E   163_B      E   163_B     2.268     0    0.076   1.163     5.830   66.905   46.138
LGA    S   164_B      S   164_B     2.462     0    0.105   0.623     6.448   57.857   46.667
LGA    N   165_B      N   165_B     1.736     0    0.379   1.195     5.503   77.143   63.750
LGA    G   166_B      G   166_B     2.955     0    0.656   0.656     4.247   52.619   52.619
LGA    Q   167_B      Q   167_B     7.295     0    0.148   1.332     9.456   10.238    5.344
LGA    P   168_B      P   168_B    10.239     0    0.071   0.357    13.006    0.357    0.408
LGA    E   169_B      E   169_B    14.619     0    0.206   1.012    15.921    0.000    0.000
LGA    N   170_B      N   170_B    15.502     0    0.614   0.702    17.348    0.000    0.000
LGA    N   171_B      N   171_B    15.575     0    0.098   1.185    19.878    0.000    0.000
LGA    Y   172_B      Y   172_B    18.468     0    0.241   1.149    21.313    0.000    0.000
LGA    K   173_B      K   173_B    19.068     0    0.057   0.964    19.539    0.000    0.000
LGA    T   174_B      T   174_B    18.839     0    0.103   1.026    18.988    0.000    0.000
LGA    T   175_B      T   175_B    19.001     0    0.187   0.246    20.142    0.000    0.000
LGA    P   176_B      P   176_B    19.553     0    0.115   0.255    22.077    0.000    0.000
LGA    P   177_B      P   177_B    17.901     0    0.057   0.173    19.380    0.000    0.000
LGA    V   178_B      V   178_B    17.935     0    0.133   1.109    21.070    0.000    0.000
LGA    L   179_B      L   179_B    18.288     0    0.589   0.525    19.737    0.000    0.000
LGA    D   180_B      D   180_B    19.314     0    0.272   0.988    21.821    0.000    0.000
LGA    S   181_B      S   181_B    26.529     0    0.249   0.607    28.747    0.000    0.000
LGA    D   182_B      D   182_B    26.369     0    0.625   1.049    27.371    0.000    0.000
LGA    G   183_B      G   183_B    20.711     0    0.232   0.232    22.737    0.000    0.000
LGA    S   184_B      S   184_B    19.235     0    0.524   0.750    22.020    0.000    0.000
LGA    F   185_B      F   185_B    18.360     0    0.099   0.140    21.482    0.000    0.000
LGA    F   186_B      F   186_B    16.382     0    0.362   1.188    17.481    0.000    0.000
LGA    L   187_B      L   187_B    14.856     0    0.097   0.999    15.191    0.000    0.000
LGA    Y   188_B      Y   188_B    12.827     0    0.050   0.892    14.991    0.000    0.000
LGA    S   189_B      S   189_B    10.576     0    0.128   0.155    11.110    0.119    0.159
LGA    K   190_B      K   190_B     9.729     0    0.094   1.359    12.531    5.952    2.646
LGA    L   191_B      L   191_B     4.073     0    0.161   0.989     8.403   28.214   25.952
LGA    T   192_B      T   192_B     3.085     0    0.095   1.031     6.808   61.429   43.197
LGA    V   193_B      V   193_B     2.860     0    0.572   0.593     6.985   69.048   48.163
LGA    D   194_B      D   194_B     2.501     0    0.243   0.865     6.565   69.286   51.905
LGA    K   195_B      K   195_B     5.033     0    0.451   1.391    12.249   26.667   13.016
LGA    S   196_B      S   196_B    10.072     0    0.608   0.608    12.501    1.429    0.952
LGA    R   197_B      R   197_B    10.470     0    0.047   0.525    17.866    0.119    0.043
LGA    W   198_B      W   198_B    10.161     0    0.038   1.490    13.449    0.119    0.102
LGA    Q   199_B      Q   199_B    13.517     0    0.611   0.976    17.400    0.000    0.000
LGA    Q   200_B      Q   200_B    19.407     0    0.582   1.125    22.285    0.000    0.000
LGA    G   201_B      G   201_B    19.942     0    0.671   0.671    21.947    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       56     224    224  100.00     449    449  100.00               255
SUMMARY(RMSD_GDC):    10.759         10.670                 11.241            4.042    2.978

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56  255    4.0     15    2.80     5.196     4.905     0.517

LGA_LOCAL      RMSD:   2.800  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.144  Number of assigned atoms:   56 
Std_ASGN_ATOMS RMSD:  10.759  Standard rmsd on all 56 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.382824 * X  +   0.056039 * Y  +  -0.922120 * Z  + 122.545731
  Y_new =  -0.837666 * X  +  -0.441970 * Y  +   0.320903 * Z  +  98.471558
  Z_new =  -0.389566 * X  +   0.895278 * Y  +   0.216138 * Z  + -35.488556 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.999466  0.400160  1.333909   [DEG: -114.5610   22.9275   76.4273 ]
ZXZ: -1.905693  1.352939 -0.410423   [DEG: -109.1882   77.5177  -23.5155 ]
 
# END of job
