
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , 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:    23       6_A - 28_A        4.98    11.19
  LONGEST_CONTINUOUS_SEGMENT:    23       7_A - 29_A        4.84    11.43
  LONGEST_CONTINUOUS_SEGMENT:    23       8_A - 30_A        4.98    11.13
  LCS_AVERAGE:     60.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      14_A - 20_A        1.11    11.03
  LCS_AVERAGE:     13.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      14_A - 19_A        0.65    10.22
  LCS_AVERAGE:     11.67

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     1_A     S     1_A      3    3   13      3    3    4    4    5    6    7    9   12   15   17   17   19   22   25   27   28   30   32   32 
LCS_GDT     D     2_A     D     2_A      3    3   13      3    3    4    4    4    5    6    8   10   15   17   17   19   22   25   27   28   30   32   32 
LCS_GDT     E     3_A     E     3_A      3    3   13      3    3    4    4    4    5    6    8   10   12   17   17   19   22   25   27   28   30   32   32 
LCS_GDT     M     4_A     M     4_A      3    3   13      3    3    3    3    5    5    6    8   10   12   17   17   19   22   25   27   28   30   32   32 
LCS_GDT     W     5_A     W     5_A      3    3   13      1    3    3    3    5    5    6    8    9   12   13   19   20   23   25   27   28   30   32   32 
LCS_GDT     F     6_A     F     6_A      3    3   23      3    3    3    3    5    6    6    7    9   12   17   21   22   23   25   27   28   30   32   32 
LCS_GDT     C     7_A     C     7_A      5    5   23      4    5    5    5    5    6    6    8    9   11   17   21   22   23   25   27   28   30   32   32 
LCS_GDT     E     8_A     E     8_A      5    5   23      4    5    5    5    6    8   10   12   15   17   19   21   22   23   24   25   27   29   32   32 
LCS_GDT     T     9_A     T     9_A      5    5   23      4    5    5    5    5    6    9   10   11   12   14   17   19   20   22   23   24   24   25   28 
LCS_GDT     L    10_A     L    10_A      5    5   23      4    5    5    5    6    8    9   11   13   17   18   21   22   23   25   27   28   30   32   32 
LCS_GDT     R    11_A     R    11_A      5    5   23      4    5    5    5    5    6    6   11   15   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     R    12_A     R    12_A      4    5   23      3    4    4    4    5    6    6    9   10   12   13   16   19   21   25   27   27   30   32   32 
LCS_GDT     L    13_A     L    13_A      4    5   23      3    4    4    5    6    8    9   12   15   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     L    14_A     L    14_A      6    7   23      4    6    8    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     C    15_A     C    15_A      6    7   23      4    6    8    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     P    16_A     P    16_A      6    7   23      4    6    8    8   11   11   13   16   16   17   19   21   22   23   25   25   28   29   32   32 
LCS_GDT     K    17_A     K    17_A      6    7   23      4    6    8    8   11   11   13   16   16   17   19   21   22   23   25   26   28   30   32   32 
LCS_GDT     S    18_A     S    18_A      6    7   23      4    6    8    8   11   11   13   16   16   17   19   21   22   23   25   26   28   30   32   32 
LCS_GDT     C    19_A     C    19_A      6    7   23      4    6    8    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     S    20_A     S    20_A      4    7   23      3    4    4    7   10   10   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     I    21_A     I    21_A      4    5   23      3    4    4    4    6    7   11   16   16   17   19   21   22   23   24   26   28   30   32   32 
LCS_GDT     E    22_A     E    22_A      4    5   23      3    4    4    5    6    9   13   16   16   17   19   21   22   23   24   26   28   30   32   32 
LCS_GDT     G    23_A     G    23_A      4    5   23      3    4    5    7   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     G    24_A     G    24_A      3    5   23      0    3    3    4    8   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     C    25_A     C    25_A      3    5   23      1    3    6    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     P    26_A     P    26_A      3    5   23      0    3    8    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     E    27_A     E    27_A      3    5   23      1    6    8    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     V    28_A     V    28_A      3    5   23      0    4    4    7   10   11   12   15   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     C    29_A     C    29_A      4    5   23      3    4    5    8   11   11   13   16   16   17   19   21   22   23   25   27   28   30   32   32 
LCS_GDT     S    30_A     S    30_A      4    4   23      3    4    4    4    7   11   13   16   16   17   18   19   21   23   25   27   28   30   32   32 
LCS_GDT     H    31_A     H    31_A      4    4   22      3    4    5    7    8   10   11   13   16   17   18   18   19   22   25   27   28   30   32   32 
LCS_GDT     M    32_A     M    32_A      4    4   21      3    4    4    4    5    6    7   10   12   16   17   18   19   22   25   27   28   30   32   32 
LCS_GDT     C    33_A     C    33_A      3    4   21      3    3    4    5    6    6    7    8   11   12   15   18   19   22   25   27   28   30   32   32 
LCS_GDT     P    34_A     P    34_A      3    4   21      3    3    4    5    6    6    7    8   11   12   13   16   17   21   25   27   27   28   31   32 
LCS_GDT     L    35_A     L    35_A      3    4   13      3    3    4    5    6    6    7    8   11   11   13   16   17   18   18   25   27   28   28   29 
LCS_AVERAGE  LCS_A:  28.63  (  11.67   13.96   60.24 )

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      6      8      8     11     11     13     16     16     17     19     21     22     23     25     27     28     30     32     32 
GDT PERCENT_AT  11.43  17.14  22.86  22.86  31.43  31.43  37.14  45.71  45.71  48.57  54.29  60.00  62.86  65.71  71.43  77.14  80.00  85.71  91.43  91.43
GDT RMS_LOCAL    0.25   0.54   0.85   0.85   1.60   1.60   2.14   2.83   2.83   3.03   3.87   4.28   4.48   4.67   5.70   5.97   5.94   6.33   6.61   6.61
GDT RMS_ALL_AT  18.64   9.96   9.94   9.94   9.85   9.85   9.72   9.86   9.86   9.75  10.60  10.27  10.45  10.10   7.59   7.57   7.82   7.57   7.60   7.60

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E     3_A      E     3_A
#   possible swapping detected:  E    22_A      E    22_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A    19.117     0    0.176   0.223    21.229    0.000    0.000
LGA    D     2_A      D     2_A    16.513     0    0.610   1.210    18.652    0.000    0.000
LGA    E     3_A      E     3_A    14.873     0    0.570   0.811    18.550    0.000    0.000
LGA    M     4_A      M     4_A    13.757     0    0.613   0.776    22.308    0.357    0.179
LGA    W     5_A      W     5_A     9.506     0    0.575   1.222    11.288    0.833    4.694
LGA    F     6_A      F     6_A     9.356     0    0.594   0.589    10.751    1.786    0.866
LGA    C     7_A      C     7_A     9.698     0    0.586   0.540    11.241    1.310    0.873
LGA    E     8_A      E     8_A    10.330     0    0.041   1.048    13.193    0.119    0.899
LGA    T     9_A      T     9_A    16.140     0    0.025   0.519    20.399    0.000    0.000
LGA    L    10_A      L    10_A    13.222     0    0.153   0.191    16.993    0.000    0.000
LGA    R    11_A      R    11_A     9.957     0    0.353   0.478    13.121    0.119    0.043
LGA    R    12_A      R    12_A    12.781     0    0.030   0.801    25.938    0.000    0.000
LGA    L    13_A      L    13_A     9.162     0    0.607   1.274    13.989    6.190    3.095
LGA    L    14_A      L    14_A     1.751     0    0.595   0.476     4.359   72.738   74.226
LGA    C    15_A      C    15_A     0.443     0    0.060   0.773     2.048   86.071   81.746
LGA    P    16_A      P    16_A     2.876     0    0.079   0.118     4.048   60.952   54.490
LGA    K    17_A      K    17_A     2.403     0    0.071   0.130     3.326   59.048   57.196
LGA    S    18_A      S    18_A     2.750     0    0.234   0.775     3.435   55.357   57.381
LGA    C    19_A      C    19_A     2.135     0    0.626   0.757     3.372   61.071   61.190
LGA    S    20_A      S    20_A     3.755     0    0.666   0.589     7.149   42.381   32.778
LGA    I    21_A      I    21_A     4.622     0    0.105   0.197     8.555   35.357   22.917
LGA    E    22_A      E    22_A     3.856     0    0.022   0.960     9.827   54.048   28.889
LGA    G    23_A      G    23_A     2.042     0    0.629   0.629     2.611   69.048   69.048
LGA    G    24_A      G    24_A     3.190     0    0.512   0.512     3.190   59.286   59.286
LGA    C    25_A      C    25_A     1.111     0    0.055   0.781     3.566   86.548   77.063
LGA    P    26_A      P    26_A     2.899     0    0.703   0.676     5.501   52.500   53.741
LGA    E    27_A      E    27_A     2.756     0    0.684   1.235     5.285   55.595   47.143
LGA    V    28_A      V    28_A     5.668     0    0.584   1.086     9.163   34.762   20.952
LGA    C    29_A      C    29_A     2.628     0    0.638   0.646     3.775   57.619   61.508
LGA    S    30_A      S    30_A     3.148     0    0.122   0.140     6.648   50.119   39.206
LGA    H    31_A      H    31_A     7.843     0    0.564   1.270    12.681    7.381    3.000
LGA    M    32_A      M    32_A     9.995     0    0.627   1.323    16.218    1.310    0.655
LGA    C    33_A      C    33_A    11.712     0    0.297   0.331    13.537    0.000    0.000
LGA    P    34_A      P    34_A    17.260     0    0.520   0.446    20.895    0.000    0.000
LGA    L    35_A      L    35_A    20.872     0    0.379   0.610    23.985    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     7.383          7.216                  9.028           28.912   26.088

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     16    2.83    40.714    34.041     0.546

LGA_LOCAL      RMSD:   2.830  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.858  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   7.383  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.853406 * X  +  -0.286827 * Y  +  -0.435234 * Z  +  -6.944254
  Y_new =  -0.501699 * X  +  -0.678517 * Y  +  -0.536575 * Z  +   0.611487
  Z_new =  -0.141409 * X  +   0.676273 * Y  +  -0.722951 * Z  +  -0.328075 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.531459  0.141885  2.389542   [DEG:  -30.4503    8.1294  136.9107 ]
ZXZ: -0.681493  2.378861 -0.206131   [DEG:  -39.0467  136.2987  -11.8104 ]
 
# END of job
