
#######################################################
#                                                     #
#                        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 (  263),  selected   35 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       7_F - 35_F        4.79     8.04
  LONGEST_CONTINUOUS_SEGMENT:    29       8_F - 36_F        4.81     7.87
  LCS_AVERAGE:     55.39

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      10_F - 29_F        1.98     9.58
  LCS_AVERAGE:     29.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      10_F - 24_F        0.88    10.27
  LONGEST_CONTINUOUS_SEGMENT:    15      11_F - 25_F        0.95    10.71
  LCS_AVERAGE:     19.01

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     R     6_F     R     6_F      3    6   12      3    3    4    5    6    6    7    7    8    8   10   10   11   11   12   12   16   19   19   20 
LCS_GDT     F     7_F     F     7_F      4    6   29      3    3    4    5    6    6    7    7    8    8   10   10   12   12   14   15   18   23   26   28 
LCS_GDT     F     8_F     F     8_F      4    6   29      3    3    4    5    6    6    7    9   10   14   25   25   26   27   27   27   28   29   31   32 
LCS_GDT     A     9_F     A     9_F      4   19   29      3    3    4    5   14   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     K    10_F     K    10_F     15   20   29      3    5    9   10   16   18   21   23   25   25   25   26   26   27   27   27   28   28   29   31 
LCS_GDT     D    11_F     D    11_F     15   20   29      7   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     M    12_F     M    12_F     15   20   29      7   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     R    13_F     R    13_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     A    14_F     A    14_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     A    15_F     A    15_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     L    16_F     L    16_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     A    17_F     A    17_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     Q    18_F     Q    18_F     15   20   29      7   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     V    19_F     V    19_F     15   20   29      8   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     K    20_F     K    20_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     D    21_F     D    21_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     T    22_F     T    22_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     L    23_F     L    23_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     G    24_F     G    24_F     15   20   29     10   14   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     S    25_F     S    25_F     15   20   29      3    4    8   14   15   16   20   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     D    26_F     D    26_F      6   20   29      3   10   15   15   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     A    27_F     A    27_F      6   20   29      3    5    6   13   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     V    28_F     V    28_F      6   20   29      3    5    7   10   15   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     I    29_F     I    29_F      6   20   29      3    5    8   14   17   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     M    30_F     M    30_F      6    9   29      3    5    6   10   12   17   19   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     S    31_F     S    31_F      6    9   29      3    4    6   11   15   20   21   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     N    32_F     N    32_F      3    9   29      3    3    4    5    8    9   19   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     K    33_F     K    33_F      4    9   29      3    4    4    5    8   11   19   23   25   25   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     K    34_F     K    34_F      4    6   29      3    4    4    5    6    7    8   12   19   24   25   26   26   27   27   27   28   29   31   32 
LCS_GDT     V    35_F     V    35_F      4    6   29      3    4    4    5    6    7    8   10   12   13   14   17   22   25   26   27   28   29   31   32 
LCS_GDT     N    36_F     N    36_F      4    6   29      3    4    4    5    5    6    8   10   12   13   14   15   16   21   25   25   28   29   31   32 
LCS_GDT     G    37_F     G    37_F      4    6   17      3    3    4    5    5    6    7    8   12   13   14   15   16   17   20   24   25   28   29   32 
LCS_GDT     G    38_F     G    38_F      4    6   17      3    3    4    4    5    7    8    9   12   13   14   15   17   21   25   25   28   29   31   32 
LCS_GDT     I    39_F     I    39_F      4    5   17      3    3    4    4    5    5    5    5    7    8    8    9   13   17   22   25   28   29   31   32 
LCS_GDT     E    40_F     E    40_F      4    5   17      0    3    4    4    5    5    5    5   10   12   14   15   16   17   22   24   28   29   31   32 
LCS_AVERAGE  LCS_A:  34.77  (  19.01   29.91   55.39 )

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     10     14     15     15     17     20     21     23     25     25     25     26     26     27     27     27     28     29     31     32 
GDT PERCENT_AT  20.41  28.57  30.61  30.61  34.69  40.82  42.86  46.94  51.02  51.02  51.02  53.06  53.06  55.10  55.10  55.10  57.14  59.18  63.27  65.31
GDT RMS_LOCAL    0.32   0.54   0.75   0.75   1.43   1.93   2.01   2.34   2.59   2.59   2.59   3.02   3.02   3.33   3.33   3.33   4.03   4.99   5.81   6.19
GDT RMS_ALL_AT  10.05  10.25  10.20  10.20   9.59   9.09   9.22   9.08   8.98   8.98   8.98   8.69   8.69   8.56   8.56   8.56   8.20   7.65   7.43   7.44

# Checking swapping
#   possible swapping detected:  D    11_F      D    11_F
#   possible swapping detected:  E    40_F      E    40_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R     6_F      R     6_F    21.429     0    0.050   1.221    24.095    0.000    0.000
LGA    F     7_F      F     7_F    15.675     0    0.116   1.236    23.918    0.000    0.000
LGA    F     8_F      F     8_F     8.611     0    0.048   1.369    11.397    5.833   25.195
LGA    A     9_F      A     9_F     3.246     0    0.086   0.129     5.032   46.071   43.143
LGA    K    10_F      K    10_F     3.361     0    0.628   1.089     7.761   50.476   30.212
LGA    D    11_F      D    11_F     1.788     0    0.017   0.970     5.135   75.000   59.940
LGA    M    12_F      M    12_F     2.223     0    0.020   1.136     7.324   68.810   51.726
LGA    R    13_F      R    13_F     1.388     0    0.037   1.203     7.356   81.548   58.312
LGA    A    14_F      A    14_F     0.952     0    0.016   0.020     1.151   88.214   86.857
LGA    A    15_F      A    15_F     1.180     0    0.051   0.053     1.495   83.690   83.238
LGA    L    16_F      L    16_F     0.966     0    0.055   0.774     3.850   88.214   77.024
LGA    A    17_F      A    17_F     1.248     0    0.083   0.091     1.619   81.429   79.714
LGA    Q    18_F      Q    18_F     2.150     0    0.028   1.496     6.601   66.786   48.677
LGA    V    19_F      V    19_F     2.095     0    0.039   0.087     2.938   70.833   66.054
LGA    K    20_F      K    20_F     1.078     0    0.028   1.402     6.764   85.952   65.767
LGA    D    21_F      D    21_F     1.598     0    0.017   0.860     4.120   75.000   62.143
LGA    T    22_F      T    22_F     2.353     0    0.100   0.137     2.726   62.857   61.497
LGA    L    23_F      L    23_F     2.715     0    0.156   1.089     6.366   64.881   55.357
LGA    G    24_F      G    24_F     1.387     0    0.587   0.587     3.739   63.571   63.571
LGA    S    25_F      S    25_F     4.722     0    0.622   0.806     8.150   47.143   33.889
LGA    D    26_F      D    26_F     1.059     0    0.592   0.826     4.218   65.833   60.298
LGA    A    27_F      A    27_F     1.889     0    0.159   0.223     4.319   77.738   69.619
LGA    V    28_F      V    28_F     2.824     0    0.038   0.086     7.054   55.952   38.367
LGA    I    29_F      I    29_F     1.603     0    0.035   0.430     7.204   77.381   51.964
LGA    M    30_F      M    30_F     4.904     0    0.613   1.135    13.690   38.810   20.357
LGA    S    31_F      S    31_F     3.058     0    0.043   0.561     5.567   48.333   44.127
LGA    N    32_F      N    32_F     4.185     0    0.562   0.732     5.710   33.333   36.012
LGA    K    33_F      K    33_F     4.375     0    0.582   1.276     8.367   24.048   47.937
LGA    K    34_F      K    34_F     8.724     0    0.230   1.181    10.330    5.119   10.476
LGA    V    35_F      V    35_F    14.438     0    0.707   1.439    17.446    0.000    0.000
LGA    N    36_F      N    36_F    18.828     0    0.105   0.834    20.859    0.000    0.000
LGA    G    37_F      G    37_F    21.424     0    0.359   0.359    23.239    0.000    0.000
LGA    G    38_F      G    38_F    18.947     0    0.048   0.048    18.947    0.000    0.000
LGA    I    39_F      I    39_F    16.214     0    0.658   1.620    18.227    0.000    0.000
LGA    E    40_F      E    40_F    14.576     0    0.242   1.422    19.804    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     263    263  100.00                49
SUMMARY(RMSD_GDC):     7.300          7.256                  8.333           33.324   29.214

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   49    4.0     23    2.34    40.306    39.245     0.944

LGA_LOCAL      RMSD:   2.336  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.076  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   7.300  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.192437 * X  +  -0.861866 * Y  +   0.469206 * Z  +  43.503296
  Y_new =  -0.025993 * X  +   0.482452 * Y  +   0.875537 * Z  + -115.811050
  Z_new =  -0.980965 * X  +   0.156290 * Y  +  -0.115244 * Z  +  13.271254 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.007335  1.375370  2.206166   [DEG: -172.3076   78.8029  126.4040 ]
ZXZ:  2.649634  1.686297 -1.412801   [DEG:  151.8129   96.6177  -80.9476 ]
 
# END of job
