
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       9_F - 33_F        4.89     5.16
  LCS_AVERAGE:     95.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.89    16.12
  LCS_AVERAGE:     42.75

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.98    17.12
  LCS_AVERAGE:     36.24

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     8_D     L     8_F      3    3   23      0    3    3    3    3    3    4    9    9   15   15   19   20   21   23   25   26   26   26   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   25      3    3    6    6    8    9   12   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     K    10_D     K    10_F      4    4   25      3    4    6    6    8    9   12   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     L    11_D     L    11_F      4   10   25      3    4    6    7    8    9   12   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     N    12_D     N    12_F      9   11   25      5    8    8    9   11   11   12   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     S    13_D     S    13_F      9   11   25      5    8    8    9   11   11   11   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     W    14_D     W    14_F      9   11   25      5    8    8    9   11   11   11   12   15   16   18   20   22   22   24   25   26   26   26   26 
LCS_GDT     D    15_D     D    15_F      9   11   25      5    8    8    9   11   11   12   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     V    16_D     V    16_F      9   11   25      5    8    8    9   11   11   12   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     F    17_D     F    17_F      9   11   25      4    8    8    9   11   11   11   12   15   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     G    18_D     G    18_F      9   11   25      4    8    8    9   11   11   11   13   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     N    19_D     N    19_F      9   11   25      3    8    8    9   11   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     W    20_D     W    20_F      9   11   25      3    5    8    9   11   11   11   12   15   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     F    21_D     F    21_F      5   13   25      3    4    5    9   11   11   13   14   14   16   18   19   21   22   24   25   26   26   26   26 
LCS_GDT     D    22_D     D    22_F     12   13   25      5    9   11   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     L    23_D     L    23_F     12   13   25      4   10   11   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     A    24_D     A    24_F     12   13   25      5   10   11   12   12   12   13   14   14   16   18   19   21   22   24   25   26   26   26   26 
LCS_GDT     S    25_D     S    25_F     12   13   25      5   10   11   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     W    26_D     W    26_F     12   13   25      6   10   11   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     I    27_D     I    27_F     12   13   25      5   10   11   12   12   12   13   14   14   16   18   19   22   22   24   25   26   26   26   26 
LCS_GDT     K    28_D     K    28_F     12   13   25      6   10   11   12   12   12   13   14   15   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   25      6   10   11   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     I    30_D     I    30_F     12   13   25      6   10   11   12   12   12   13   14   14   16   18   19   22   22   24   25   26   26   26   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   25      6   10   11   12   12   12   13   14   14   15   17   19   21   22   24   25   26   26   26   26 
LCS_GDT     R    32_D     R    32_F     12   13   25      6   10   11   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_GDT     R    33_D     R    33_F     12   13   25      3    3    8   12   12   12   13   14   16   17   19   20   22   22   24   25   26   26   26   26 
LCS_AVERAGE  LCS_A:  58.28  (  36.24   42.75   95.86 )

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      6     10     11     12     12     12     13     14     16     17     19     20     22     22     24     25     26     26     26     26 
GDT PERCENT_AT  23.08  38.46  42.31  46.15  46.15  46.15  50.00  53.85  61.54  65.38  73.08  76.92  84.62  84.62  92.31  96.15 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.70   0.75   0.98   0.98   0.98   1.69   2.07   3.38   3.55   3.85   4.01   4.39   4.39   4.72   4.89   5.10   5.10   5.10   5.10
GDT RMS_ALL_AT  18.72  16.93  16.72  17.12  17.12  17.12  15.52  15.15   5.23   5.47   5.20   5.22   5.14   5.14   5.15   5.16   5.10   5.10   5.10   5.10

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    36.058     0    0.282   1.517    38.104    0.000    0.000
LGA    Q     9_D      Q     9_F    33.141     0    0.548   1.051    36.758    0.000    0.000
LGA    K    10_D      K    10_F    30.091     0    0.031   0.896    34.872    0.000    0.000
LGA    L    11_D      L    11_F    23.941     0    0.594   0.523    26.401    0.000    0.000
LGA    N    12_D      N    12_F    22.979     0    0.569   0.993    28.784    0.000    0.000
LGA    S    13_D      S    13_F    22.034     0    0.041   0.075    26.353    0.000    0.000
LGA    W    14_D      W    14_F    19.124     0    0.074   0.153    20.673    0.000    0.000
LGA    D    15_D      D    15_F    14.666     0    0.088   1.125    16.822    0.000    0.000
LGA    V    16_D      V    16_F    11.825     0    0.031   1.062    14.356    0.119    0.068
LGA    F    17_D      F    17_F    13.244     0    0.052   1.458    16.063    0.119    0.043
LGA    G    18_D      G    18_F     8.636     0    0.164   0.164    10.424   15.357   15.357
LGA    N    19_D      N    19_F     3.037     0    0.261   1.136     5.475   42.381   54.821
LGA    W    20_D      W    20_F     6.998     0    0.179   1.193    17.240   15.952    4.592
LGA    F    21_D      F    21_F     4.160     0    0.541   0.963     8.917   40.714   24.242
LGA    D    22_D      D    22_F     2.938     0    0.568   1.169     8.762   65.119   37.679
LGA    L    23_D      L    23_F     1.210     0    0.120   1.239     3.369   83.690   75.476
LGA    A    24_D      A    24_F     0.943     0    0.037   0.055     1.406   85.952   85.048
LGA    S    25_D      S    25_F     2.419     0    0.156   0.708     3.661   66.786   63.889
LGA    W    26_D      W    26_F     2.379     0    0.029   0.965     3.291   68.810   66.224
LGA    I    27_D      I    27_F     1.224     0    0.056   1.266     4.075   85.952   70.357
LGA    K    28_D      K    28_F     0.371     0    0.066   0.893     4.142  100.000   86.138
LGA    Y    29_D      Y    29_F     0.877     0    0.063   0.521     3.172   92.857   74.365
LGA    I    30_D      I    30_F     0.482     0    0.059   0.744     3.467   95.238   84.405
LGA    Q    31_D      Q    31_F     1.012     0    0.101   0.646     3.576   83.690   70.952
LGA    R    32_D      R    32_F     1.075     0    0.482   1.447     5.644   79.286   66.364
LGA    R    33_D      R    33_F     2.500     0    0.581   1.080    11.425   64.881   32.121

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     5.104          4.748                  7.441           41.804   35.082

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     14    2.07    58.654    54.261     0.645

LGA_LOCAL      RMSD:   2.072  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.154  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.104  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.260887 * X  +   0.473360 * Y  +   0.841349 * Z  + -81.302689
  Y_new =   0.716436 * X  +  -0.679079 * Y  +   0.159910 * Z  + -91.170624
  Z_new =   0.647038 * X  +   0.561054 * Y  +  -0.516295 * Z  +  56.885822 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.221576 -0.703693  2.314672   [DEG:   69.9911  -40.3187  132.6210 ]
ZXZ:  1.758620  2.113315  0.856452   [DEG:  100.7615  121.0840   49.0711 ]
 
# END of job
