
#######################################################
#                                                     #
#                        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   38 (  303),  selected   38 , name one
# Molecule2: number of CA atoms  198 ( 1543),  selected   38 , 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:    22     130_A - 151_A       4.89    10.54
  LONGEST_CONTINUOUS_SEGMENT:    22     131_A - 152_A       4.76    11.20
  LCS_AVERAGE:     10.02

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12     134_A - 145_A       1.97    14.47
  LONGEST_CONTINUOUS_SEGMENT:    12     135_A - 146_A       1.89    15.23
  LCS_AVERAGE:      4.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6     133_A - 138_A       1.00    13.06
  LCS_AVERAGE:      2.33

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   38
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     S   125_A     S   125_A      3    7   15      0    3    5    6    7    9   10   11   13   18   20   21   21   23   25   26   28   30   32   33 
LCS_GDT     N   126_A     N   126_A      4    7   20      3    4    5    6    7    9   10   12   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     I   127_A     I   127_A      4    7   21      3    4    6    7    8    9   12   12   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     T   128_A     T   128_A      4    7   21      3    4    5    6    7   10   12   12   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     L   129_A     L   129_A      4   10   21      3    4    5    7    9   10   12   12   12   15   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     F   130_A     F   130_A      4   10   22      3    4    6    7    9   10   12   12   12   15   20   20   22   23   27   27   28   30   32   33 
LCS_GDT     D   131_A     D   131_A      4   10   22      3    4    5    6    9   10   12   12   12   17   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     V   132_A     V   132_A      4   10   22      3    4    4    7    7    9   12   13   16   17   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     Q   133_A     Q   133_A      6   10   22      4    5    6    9   11   12   13   14   16   17   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     E   134_A     E   134_A      6   12   22      4    5    6    9   11   12   13   15   16   17   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     Y   135_A     Y   135_A      6   12   22      4    5    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     S   136_A     S   136_A      6   12   22      4    5    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     V   137_A     V   137_A      6   12   22      4    5    6    9   10   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     S   138_A     S   138_A      6   12   22      4    4    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     D   139_A     D   139_A      4   12   22      3    4    5    8   11   12   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     N   140_A     N   140_A      4   12   22      3    4    6    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     T   141_A     T   141_A      5   12   22      3    4    6    8   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     I   142_A     I   142_A      5   12   22      4    5    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     T   143_A     T   143_A      5   12   22      4    5    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     V   144_A     V   144_A      5   12   22      4    5    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     T   145_A     T   145_A      5   12   22      4    5    7    9   11   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     P   146_A     P   146_A      5   12   22      3    4    5    8   11   13   14   15   16   16   20   21   21   24   27   27   28   30   32   33 
LCS_GDT     K   147_A     K   147_A      4    9   22      3    4    4    6    9   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     I   148_A     I   148_A      4    7   22      3    4    4    5    9   13   14   15   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     P   149_A     P   149_A      4    6   22      3    4    6    7    8    9   11   13   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     P   150_A     P   150_A      5    6   22      4    5    6    7    8    9   11   12   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     C   151_A     C   151_A      5    6   22      4    5    5    7    7    8    9   12   16   19   20   21   22   24   27   27   28   30   32   33 
LCS_GDT     T   152_A     T   152_A      5    8   22      4    5    5    5    7    8    8   10   12   12   16   17   22   24   27   27   28   30   32   33 
LCS_GDT     T   153_A     T   153_A      5    8   15      4    5    5    6    7    8    8   10   12   12   12   13   14   15   15   16   16   21   24   24 
LCS_GDT     G   154_A     G   154_A      5    8   15      4    5    6    6    7    8    8   10   12   12   12   13   14   15   15   16   16   17   17   20 
LCS_GDT     T   155_A     T   155_A      5    8   15      4    5    6    6    7    8    8   10   12   12   12   13   14   15   16   22   24   27   31   33 
LCS_GDT     W   156_A     W   156_A      5    8   15      4    5    6    6    7    8    8   10   12   12   12   14   15   18   21   22   25   30   32   33 
LCS_GDT     K   157_A     K   157_A      5    8   15      4    5    6    6    7    8    8   10   12   13   16   17   19   22   22   24   28   30   32   33 
LCS_GDT     P   158_A     P   158_A      5    8   15      4    5    6    6    7    8    8   10   12   14   16   18   19   22   22   23   25   29   32   33 
LCS_GDT     W   159_A     W   159_A      4    8   15      3    3    6    6    7    8    8   10   12   13   16   18   19   22   22   22   25   26   28   32 
LCS_GDT     H   160_A     H   160_A      3    8   15      3    3    3    3    5    8    8   10   12   14   16   18   19   22   22   23   25   29   32   33 
LCS_GDT     N   161_A     N   161_A      3    4   15      3    3    3    3    4    5    6    7    9   10   15   17   18   22   22   22   25   25   26   30 
LCS_GDT     D   162_A     D   162_A      3    4   15      3    3    3    3    6    7    8    9   10   13   16   17   19   22   22   22   25   25   25   27 
LCS_AVERAGE  LCS_A:   5.66  (   2.33    4.63   10.02 )

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      4      5      7      9     11     13     14     15     16     19     20     21     22     24     27     27     28     30     32     33 
GDT PERCENT_AT   2.02   2.53   3.54   4.55   5.56   6.57   7.07   7.58   8.08   9.60  10.10  10.61  11.11  12.12  13.64  13.64  14.14  15.15  16.16  16.67
GDT RMS_LOCAL    0.15   0.43   0.88   1.18   1.63   2.19   2.36   2.49   2.69   3.96   4.03   4.17   4.46   4.89   5.31   5.31   5.63   6.03   6.55   6.75
GDT RMS_ALL_AT  18.88  19.34  15.02  14.00  14.05  14.95  14.99  15.02  14.60   9.23   9.39   9.25   9.47   9.42   9.23   9.23   8.91   8.78   8.54   8.49

# Checking swapping
#   possible swapping detected:  D   162_A      D   162_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S   125_A      S   125_A    27.301     0    0.085   0.102    28.375    0.000    0.000
LGA    N   126_A      N   126_A    25.373     0    0.443   0.431    29.057    0.000    0.000
LGA    I   127_A      I   127_A    23.987     0    0.058   1.288    28.967    0.000    0.000
LGA    T   128_A      T   128_A    20.872     0    0.485   0.907    23.162    0.000    0.000
LGA    L   129_A      L   129_A    24.758     0    0.491   1.440    30.707    0.000    0.000
LGA    F   130_A      F   130_A    20.633     0    0.639   1.293    29.186    0.000    0.000
LGA    D   131_A      D   131_A    14.818     0    0.024   1.099    17.140    0.000    0.000
LGA    V   132_A      V   132_A     9.665     0    0.604   0.609    11.445    5.952    4.490
LGA    Q   133_A      Q   133_A     5.139     0    0.607   1.064     6.984   28.452   33.016
LGA    E   134_A      E   134_A     3.653     0    0.069   0.238     6.951   48.690   32.910
LGA    Y   135_A      Y   135_A     1.746     0    0.159   1.419     6.983   75.119   59.881
LGA    S   136_A      S   136_A     1.099     0    0.137   0.666     3.724   73.214   69.603
LGA    V   137_A      V   137_A     2.789     0    0.067   0.111     6.599   71.071   50.748
LGA    S   138_A      S   138_A     1.616     0    0.043   0.708     3.164   70.833   66.349
LGA    D   139_A      D   139_A     3.641     0    0.495   0.920     5.651   45.476   34.643
LGA    N   140_A      N   140_A     2.676     0    0.646   1.052     8.210   59.167   37.381
LGA    T   141_A      T   141_A     3.049     0    0.141   0.194     5.268   50.119   42.177
LGA    I   142_A      I   142_A     0.983     0    0.045   0.128     2.501   81.548   74.226
LGA    T   143_A      T   143_A     1.496     0    0.111   0.137     1.874   77.143   75.306
LGA    V   144_A      V   144_A     1.609     0    0.131   1.188     2.878   72.976   68.435
LGA    T   145_A      T   145_A     1.396     0    0.244   1.117     4.571   77.262   65.034
LGA    P   146_A      P   146_A     2.955     0    0.036   0.318     5.852   73.452   54.830
LGA    K   147_A      K   147_A     3.191     0    0.271   1.249    13.473   47.143   25.291
LGA    I   148_A      I   148_A     2.960     0    0.161   1.130     5.770   40.476   49.583
LGA    P   149_A      P   149_A     9.462     0    0.189   0.417    10.782    3.214    3.469
LGA    P   150_A      P   150_A    14.383     0    0.689   0.605    16.951    0.000    0.000
LGA    C   151_A      C   151_A    14.840     0    0.549   0.759    19.047    0.000    0.000
LGA    T   152_A      T   152_A    15.779     0    0.315   1.009    18.193    0.000    0.000
LGA    T   153_A      T   153_A    20.450     0    0.128   0.178    23.107    0.000    0.000
LGA    G   154_A      G   154_A    21.816     0    0.399   0.399    21.816    0.000    0.000
LGA    T   155_A      T   155_A    16.692     0    0.102   0.127    18.038    0.000    0.000
LGA    W   156_A      W   156_A    14.673     0    0.119   1.239    16.170    0.000    0.000
LGA    K   157_A      K   157_A    12.928     0    0.127   0.621    13.705    0.000    0.000
LGA    P   158_A      P   158_A    16.319     0    0.592   0.624    18.370    0.000    0.000
LGA    W   159_A      W   159_A    19.313     0    0.450   1.126    23.320    0.000    0.000
LGA    H   160_A      H   160_A    20.516     0    0.498   1.241    23.785    0.000    0.000
LGA    N   161_A      N   161_A    25.563     0    0.308   1.138    27.748    0.000    0.000
LGA    D   162_A      D   162_A    25.729     0    0.528   1.186    28.780    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       38     152    152  100.00     303    303  100.00               198
SUMMARY(RMSD_GDC):     8.223          8.263                  9.168            5.057    4.280

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38  198    4.0     15    2.49     7.071     6.679     0.579

LGA_LOCAL      RMSD:   2.492  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.016  Number of assigned atoms:   38 
Std_ASGN_ATOMS RMSD:   8.223  Standard rmsd on all 38 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.987805 * X  +  -0.052997 * Y  +  -0.146398 * Z  +  92.360802
  Y_new =   0.143097 * X  +   0.061508 * Y  +  -0.987796 * Z  +  75.023071
  Z_new =   0.061355 * X  +  -0.996699 * Y  +  -0.053174 * Z  + 200.112579 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.997730 -0.061393 -1.624096   [DEG:  171.7573   -3.5176  -93.0539 ]
ZXZ: -0.147136  1.623996  3.080112   [DEG:   -8.4303   93.0481  176.4774 ]
 
# END of job
