
#######################################################
#                                                     #
#                        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 (  283),  selected   35 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      23_B - 57_B        2.46     2.46
  LCS_AVERAGE:     57.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      29_B - 57_B        1.99     2.53
  LCS_AVERAGE:     45.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      35_B - 57_B        0.82     2.86
  LCS_AVERAGE:     32.65

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     P    23_B     P    23_B     14   21   35     12   13   13   15   21   21   23   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D    24_B     D    24_B     14   21   35     12   19   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     A    25_B     A    25_B     14   21   35     12   14   19   23   24   26   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     Q    26_B     Q    26_B     14   21   35     12   13   13   15   21   21   23   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     R    27_B     R    27_B     14   21   35     12   13   13   15   21   27   28   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    28_B     V    28_B     14   21   35     12   13   13   25   26   26   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     A    29_B     A    29_B     14   29   35     12   13   13   15   22   23   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D    30_B     D    30_B     14   29   35     12   13   13   15   21   21   28   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    31_B     E    31_B     14   29   35     12   13   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    32_B     L    32_B     14   29   35     12   13   13   15   24   26   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     M    33_B     M    33_B     14   29   35     12   13   13   15   21   21   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    34_B     K    34_B     14   29   35     12   13   13   15   21   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    35_B     K    35_B     23   29   35      3   13   17   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    36_B     L    36_B     23   29   35      3   17   22   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     F    37_B     F    37_B     23   29   35      3   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D    38_B     D    38_B     23   29   35      5   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     A    39_B     A    39_B     23   29   35     10   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     A    40_B     A    40_B     23   29   35      6   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     H    41_B     H    41_B     23   29   35     11   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     R    42_B     R    42_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     N    43_B     N    43_B     23   29   35      5   19   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D    44_B     D    44_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    45_B     K    45_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D    46_B     D    46_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    47_B     K    47_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    48_B     V    48_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    49_B     K    49_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    50_B     K    50_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    51_B     V    51_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    52_B     V    52_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    53_B     E    53_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    54_B     E    54_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     A    55_B     A    55_B     23   29   35     13   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    56_B     K    56_B     23   29   35      8   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    57_B     K    57_B     23   29   35      8   20   23   25   26   27   29   35   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_AVERAGE  LCS_A:  45.11  (  32.65   45.29   57.38 )

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     13     20     23     25     26     27     29     35     35     35     35     35     35     35     35     35     35     35     35     35 
GDT PERCENT_AT  21.31  32.79  37.70  40.98  42.62  44.26  47.54  57.38  57.38  57.38  57.38  57.38  57.38  57.38  57.38  57.38  57.38  57.38  57.38  57.38
GDT RMS_LOCAL    0.20   0.56   0.83   0.95   1.03   1.33   1.61   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46
GDT RMS_ALL_AT   2.77   2.81   2.87   2.88   2.90   2.83   2.74   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46

# Checking swapping
#   possible swapping detected:  F    37_B      F    37_B
#   possible swapping detected:  D    44_B      D    44_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P    23_B      P    23_B     4.619     0    0.180   0.333     6.525   40.476   31.973
LGA    D    24_B      D    24_B     2.724     0    0.108   0.455     7.402   62.976   42.738
LGA    A    25_B      A    25_B     3.998     0    0.029   0.026     6.036   47.143   41.143
LGA    Q    26_B      Q    26_B     4.693     0    0.085   1.405    11.205   40.357   21.376
LGA    R    27_B      R    27_B     3.695     0    0.038   1.564    13.482   55.595   23.074
LGA    V    28_B      V    28_B     3.416     0    0.020   0.037     7.223   55.476   38.776
LGA    A    29_B      A    29_B     4.297     0    0.014   0.015     6.167   46.905   40.952
LGA    D    30_B      D    30_B     3.965     0    0.029   0.774     9.558   50.119   28.750
LGA    E    31_B      E    31_B     3.036     0    0.017   1.038     8.506   61.190   35.291
LGA    L    32_B      L    32_B     3.741     0    0.047   1.399     8.792   50.357   33.631
LGA    M    33_B      M    33_B     3.914     0    0.027   1.064    11.780   51.905   29.881
LGA    K    34_B      K    34_B     3.256     0    0.147   0.350     9.552   57.381   31.905
LGA    K    35_B      K    35_B     2.685     0    0.228   0.380    10.025   66.905   38.571
LGA    L    36_B      L    36_B     1.753     0    0.142   1.161     3.624   79.286   72.440
LGA    F    37_B      F    37_B     1.235     0    0.027   1.188     6.291   81.429   57.446
LGA    D    38_B      D    38_B     1.472     0    0.014   0.183     2.006   81.429   76.131
LGA    A    39_B      A    39_B     1.043     0    0.032   0.032     1.184   81.429   83.238
LGA    A    40_B      A    40_B     1.213     0    0.093   0.098     1.676   79.286   79.714
LGA    H    41_B      H    41_B     1.481     0    0.089   0.928     3.543   79.286   70.238
LGA    R    42_B      R    42_B     0.865     0    0.191   1.945     9.582   85.952   53.377
LGA    N    43_B      N    43_B     1.636     0    0.197   0.251     3.282   79.405   68.333
LGA    D    44_B      D    44_B     0.691     0    0.045   0.181     1.037   92.976   91.726
LGA    K    45_B      K    45_B     0.455     0    0.020   0.286     1.015   95.238   91.640
LGA    D    46_B      D    46_B     0.955     0    0.007   0.035     1.714   90.476   82.738
LGA    K    47_B      K    47_B     0.348     0    0.027   0.270     1.203   97.619   93.757
LGA    V    48_B      V    48_B     0.422     0    0.030   0.071     0.815   95.238   95.918
LGA    K    49_B      K    49_B     1.007     0    0.054   0.971     5.022   83.690   66.190
LGA    K    50_B      K    50_B     0.970     0    0.028   0.831     5.364   88.214   68.995
LGA    V    51_B      V    51_B     0.622     0    0.023   0.086     0.952   90.476   93.197
LGA    V    52_B      V    52_B     1.215     0    0.013   0.079     1.793   81.429   80.204
LGA    E    53_B      E    53_B     1.423     0    0.027   0.332     1.830   79.286   79.524
LGA    E    54_B      E    54_B     1.226     0    0.047   0.954     4.272   81.429   70.265
LGA    A    55_B      A    55_B     1.413     0    0.091   0.095     1.871   77.143   78.000
LGA    K    56_B      K    56_B     1.524     0    0.065   0.845     5.308   77.143   61.323
LGA    K    57_B      K    57_B     1.237     0    0.534   0.494     2.758   75.357   77.778

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     283    283  100.00                61
SUMMARY(RMSD_GDC):     2.465          2.154                  3.987           41.639   34.922

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   61    4.0     35    2.46    47.131    47.461     1.365

LGA_LOCAL      RMSD:   2.465  Number of atoms:   35  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.465  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   2.465  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.839781 * X  +   0.496726 * Y  +  -0.219159 * Z  +  30.111084
  Y_new =   0.447171 * X  +   0.861742 * Y  +   0.239662 * Z  + -26.157341
  Z_new =   0.307905 * X  +   0.103262 * Y  +  -0.945797 * Z  + -11.559687 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.652296 -0.312990  3.032843   [DEG:  151.9653  -17.9330  173.7691 ]
ZXZ: -2.400852  2.810836  1.247214   [DEG: -137.5587  161.0490   71.4601 ]
 
# END of job
