
#######################################################
#                                                     #
#                        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:    24      12_A - 35_A        4.84     7.61
  LCS_AVERAGE:     60.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      17_A - 25_A        1.93    13.36
  LCS_AVERAGE:     16.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      16_A - 22_A        0.87    14.57
  LCS_AVERAGE:     12.33

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    4   12      3    3    3    3    4    4    4   12   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     D     2_A     D     2_A      3    4   12      3    3    3    3    4    4    4    6   12   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     E     3_A     E     3_A      3    4   12      3    3    3    3    4    4    6    8    9    9   13   17   22   24   25   27   29   30   32   33 
LCS_GDT     M     4_A     M     4_A      3    4   12      3    3    4    4    4    5    6    8    9   13   18   20   22   24   25   27   29   30   32   33 
LCS_GDT     W     5_A     W     5_A      3    3   12      3    3    4    4    4    5    6    8    9    9   14   16   19   22   25   27   29   30   32   33 
LCS_GDT     F     6_A     F     6_A      3    3   17      3    3    4    4    4    5    6    8    9   10   12   16   19   22   25   27   29   30   32   33 
LCS_GDT     C     7_A     C     7_A      5    5   17      4    5    5    5    5    5    6    8    9   10   12   13   19   21   24   26   29   30   32   33 
LCS_GDT     E     8_A     E     8_A      5    5   17      4    5    5    5    5    5    6    9   10   13   14   14   15   19   20   23   25   27   30   31 
LCS_GDT     T     9_A     T     9_A      5    5   17      4    5    5    5    5    5    6    8   10   13   14   14   15   16   19   19   20   26   27   28 
LCS_GDT     L    10_A     L    10_A      5    5   17      4    5    5    5    5    5    6    8   10   13   14   14   17   21   24   27   29   30   32   33 
LCS_GDT     R    11_A     R    11_A      5    5   23      4    5    5    5    5    5    6    9   12   16   18   19   21   22   25   27   29   30   32   33 
LCS_GDT     R    12_A     R    12_A      3    4   24      3    3    3    5    8    9   11   16   16   17   19   20   22   24   25   27   29   30   32   33 
LCS_GDT     L    13_A     L    13_A      3    4   24      3    4    5    8   10   10   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     L    14_A     L    14_A      4    4   24      3    4    4    4    4    7    9   13   16   17   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     C    15_A     C    15_A      4    8   24      3    4    4    4    4    8   11   12   16   17   19   19   22   24   25   27   28   29   32   33 
LCS_GDT     P    16_A     P    16_A      7    8   24      3    4    7    7    8   11   12   13   13   14   17   19   21   23   24   25   28   28   32   33 
LCS_GDT     K    17_A     K    17_A      7    9   24      3    6    7    8   10   11   12   13   16   17   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     S    18_A     S    18_A      7    9   24      5    6    7    8   10   11   12   14   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     C    19_A     C    19_A      7    9   24      5    6    7    7   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     S    20_A     S    20_A      7    9   24      5    6    7    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     I    21_A     I    21_A      7    9   24      5    6    7    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     E    22_A     E    22_A      7    9   24      5    6    7    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   31   33 
LCS_GDT     G    23_A     G    23_A      4    9   24      3    4    6    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     G    24_A     G    24_A      4    9   24      3    4    6    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     C    25_A     C    25_A      3    9   24      3    4    6    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     P    26_A     P    26_A      4    7   24      3    4    4    5    8    8   12   14   15   17   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     E    27_A     E    27_A      4    6   24      3    4    4    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     V    28_A     V    28_A      4    6   24      3    4    4    5   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     C    29_A     C    29_A      4    6   24      3    4    5    8   10   11   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     S    30_A     S    30_A      3    6   24      3    3    7    7    9    9   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     H    31_A     H    31_A      3    4   24      3    3    3    5    7   10   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     M    32_A     M    32_A      3    4   24      3    3    3    3    9   10   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     C    33_A     C    33_A      3    4   24      3    3    4    4    5    9   12   16   16   18   19   21   22   24   25   27   29   30   32   33 
LCS_GDT     P    34_A     P    34_A      3    4   24      3    3    3    3    4    5    6    7   12   14   18   20   22   24   25   27   28   30   32   33 
LCS_GDT     L    35_A     L    35_A      3    4   24      3    3    3    3    4    5    8   11   14   16   19   20   22   24   25   27   29   30   32   33 
LCS_AVERAGE  LCS_A:  29.99  (  12.33   16.90   60.73 )

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      6      7      8     10     11     12     16     16     18     19     21     22     24     25     27     29     30     32     33 
GDT PERCENT_AT  14.29  17.14  20.00  22.86  28.57  31.43  34.29  45.71  45.71  51.43  54.29  60.00  62.86  68.57  71.43  77.14  82.86  85.71  91.43  94.29
GDT RMS_LOCAL    0.21   0.40   0.87   1.52   1.78   2.01   2.19   3.03   3.01   3.32   3.51   3.85   4.03   4.60   4.76   5.06   5.66   5.95   6.24   6.27
GDT RMS_ALL_AT  13.01  13.51  14.57   8.19   8.19  14.58  11.66   7.39   7.61   7.53   7.42   7.57   7.71   7.61   7.46   7.29   6.94   6.86   6.91   6.90

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E     3_A      E     3_A
#   possible swapping detected:  E     8_A      E     8_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     6.901     0    0.284   0.316     9.500   11.786    8.333
LGA    D     2_A      D     2_A     7.193     0    0.494   1.189     8.759   11.667    8.631
LGA    E     3_A      E     3_A     8.743     0    0.570   0.778    12.061    4.405    2.011
LGA    M     4_A      M     4_A     7.110     0    0.616   1.108     9.706   12.857    8.988
LGA    W     5_A      W     5_A     9.905     0    0.576   1.143    18.464    2.143    0.612
LGA    F     6_A      F     6_A    10.839     0    0.605   0.638    12.779    0.000    0.000
LGA    C     7_A      C     7_A    11.901     0    0.586   0.516    14.151    0.000    0.000
LGA    E     8_A      E     8_A    13.081     0    0.096   0.950    19.248    0.000    0.000
LGA    T     9_A      T     9_A    15.225     0    0.032   0.149    18.637    0.000    0.000
LGA    L    10_A      L    10_A    11.661     0    0.197   0.177    16.489    1.548    0.774
LGA    R    11_A      R    11_A     8.172     0    0.438   0.541    19.693   11.190    4.069
LGA    R    12_A      R    12_A     4.017     0    0.659   0.935    10.360   43.333   21.255
LGA    L    13_A      L    13_A     3.506     0    0.621   0.987     6.146   42.024   35.655
LGA    L    14_A      L    14_A     8.187     0    0.661   0.554    11.566    7.381    4.107
LGA    C    15_A      C    15_A     9.526     0    0.011   0.877    10.347    2.381    1.667
LGA    P    16_A      P    16_A    10.855     0    0.603   0.697    13.568    1.310    0.748
LGA    K    17_A      K    17_A     8.957     0    0.105   0.748    13.500    9.524    4.233
LGA    S    18_A      S    18_A     5.632     0    0.080   0.084     8.752   33.810   24.683
LGA    C    19_A      C    19_A     2.210     0    0.026   0.121     3.748   67.738   71.032
LGA    S    20_A      S    20_A     3.684     0    0.052   0.715     5.908   45.476   38.254
LGA    I    21_A      I    21_A     2.133     0    0.112   0.238     6.722   68.929   53.750
LGA    E    22_A      E    22_A     3.133     0    0.275   1.191     6.301   51.905   37.778
LGA    G    23_A      G    23_A     2.949     0    0.697   0.697     3.080   61.190   61.190
LGA    G    24_A      G    24_A     2.094     0    0.151   0.151     2.364   77.619   77.619
LGA    C    25_A      C    25_A     0.918     0    0.526   0.800     3.487   75.714   75.476
LGA    P    26_A      P    26_A     5.851     0    0.689   0.605     8.379   26.548   19.592
LGA    E    27_A      E    27_A     3.319     0    0.097   1.036     5.094   46.667   40.212
LGA    V    28_A      V    28_A     3.768     0    0.252   0.558     5.207   45.000   39.252
LGA    C    29_A      C    29_A     1.659     0    0.583   0.792     2.924   69.048   70.397
LGA    S    30_A      S    30_A     3.159     0    0.599   0.890     6.575   55.833   43.016
LGA    H    31_A      H    31_A     3.063     0    0.436   1.413    11.351   59.167   28.381
LGA    M    32_A      M    32_A     3.017     0    0.589   1.365     3.594   55.357   55.774
LGA    C    33_A      C    33_A     3.891     0    0.277   0.303     7.021   30.714   26.270
LGA    P    34_A      P    34_A     8.532     0    0.475   0.411    10.086    7.381    7.075
LGA    L    35_A      L    35_A     9.014     0    0.367   0.534    12.504    1.548    4.524

# 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):     6.841          6.631                  8.261           29.748   25.010

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     16    3.03    40.714    34.450     0.511

LGA_LOCAL      RMSD:   3.028  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.391  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   6.841  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.744922 * X  +   0.428463 * Y  +  -0.511382 * Z  +  -6.785130
  Y_new =   0.597632 * X  +  -0.087869 * Y  +   0.796941 * Z  +  -3.864591
  Z_new =   0.296525 * X  +  -0.899277 * Y  +  -0.321519 * Z  +  -3.778108 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.676127 -0.301052 -1.914164   [DEG:   38.7392  -17.2490 -109.6735 ]
ZXZ: -2.571088  1.898129  2.823082   [DEG: -147.3125  108.7548  161.7507 ]
 
# END of job
