
#######################################################
#                                                     #
#                        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   29 (  260),  selected   25 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   25 , 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       8_F - 32_F        4.74     4.74
  LCS_AVERAGE:     96.15

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      21_F - 32_F        1.65     6.48
  LCS_AVERAGE:     33.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      22_F - 32_F        0.69     6.61
  LCS_AVERAGE:     27.38

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   25
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    5   25      0    3    3    3    4    5    6    7    7    7    7   12   14   15   16   17   20   23   23   25 
LCS_GDT     Q     9_D     Q     9_F      4    5   25      3    4    4    4    4    7   10   13   14   16   19   21   22   23   24   24   24   24   24   25 
LCS_GDT     K    10_D     K    10_F      4    6   25      3    4    4    4    5    6    7    7   11   11   19   20   22   23   24   24   24   24   24   25 
LCS_GDT     L    11_D     L    11_F      5    6   25      3    4    5    5    5    6    7    9    9   19   20   21   22   23   24   24   24   24   24   25 
LCS_GDT     N    12_D     N    12_F      5    6   25      4    4    5    5    5   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     S    13_D     S    13_F      5    6   25      4    4    5    5    5   16   16   16   17   19   21   21   22   22   24   24   24   24   24   25 
LCS_GDT     W    14_D     W    14_F      5    6   25      4    4   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     D    15_D     D    15_F      5    6   25      4    4    5    9   11   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     V    16_D     V    16_F      3    6   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     F    17_D     F    17_F      3    4   25      0    3    3   12   13   14   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     G    18_D     G    18_F      3    5   25      0    3    3    5    7   12   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     N    19_D     N    19_F      4    5   25      3    3   11   12   13   14   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     W    20_D     W    20_F      4    5   25      3    3    4    4    4    7   10   12   14   16   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     F    21_D     F    21_F      4   12   25      3    3    4    5   11   13   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     D    22_D     D    22_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     L    23_D     L    23_F     11   12   25      4   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     A    24_D     A    24_F     11   12   25      4   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     S    25_D     S    25_F     11   12   25      4   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     W    26_D     W    26_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     I    27_D     I    27_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     K    28_D     K    28_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     Y    29_D     Y    29_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     I    30_D     I    30_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     Q    31_D     Q    31_F     11   12   25      7   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_GDT     R    32_D     R    32_F     11   12   25      8   10   12   13   13   16   16   18   19   19   21   21   22   23   24   24   24   24   24   25 
LCS_AVERAGE  LCS_A:  52.21  (  27.38   33.08   96.15 )

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      8     10     12     13     13     16     16     18     19     19     21     21     22     23     24     24     24     24     24     25 
GDT PERCENT_AT  30.77  38.46  46.15  50.00  50.00  61.54  61.54  69.23  73.08  73.08  80.77  80.77  84.62  88.46  92.31  92.31  92.31  92.31  92.31  96.15
GDT RMS_LOCAL    0.36   0.49   0.83   0.98   0.98   1.60   1.60   2.36   2.49   2.48   3.06   3.06   3.35   3.94   4.19   4.19   4.19   4.19   4.19   4.74
GDT RMS_ALL_AT   5.66   5.72   6.71   6.30   6.30   6.20   6.20   5.31   5.54   5.82   5.69   5.69   5.40   4.76   4.82   4.82   4.82   4.82   4.82   4.74

# Checking swapping
#   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    14.164     0    0.262   1.056    16.669    0.000    0.000
LGA    Q     9_D      Q     9_F    10.473     0    0.623   1.044    11.695    0.000    0.000
LGA    K    10_D      K    10_F    11.292     0    0.050   0.752    19.202    0.119    0.053
LGA    L    11_D      L    11_F     7.149     0    0.604   0.587    11.049   18.690   12.976
LGA    N    12_D      N    12_F     3.754     0    0.121   0.970     5.108   35.833   43.929
LGA    S    13_D      S    13_F     6.497     0    0.086   0.719     8.214   20.476   15.635
LGA    W    14_D      W    14_F     4.527     0    0.425   1.270     9.163   33.095   17.891
LGA    D    15_D      D    15_F     3.364     0    0.647   0.712     5.843   41.190   37.738
LGA    V    16_D      V    16_F     2.852     0    0.567   1.415     6.761   67.143   47.823
LGA    F    17_D      F    17_F     2.470     0    0.633   1.332    10.412   75.357   34.329
LGA    G    18_D      G    18_F     3.732     0    0.686   0.686     4.324   43.452   43.452
LGA    N    19_D      N    19_F     3.002     0    0.712   1.323     7.033   48.333   32.976
LGA    W    20_D      W    20_F     7.223     0    0.122   1.103    16.162   14.167    4.082
LGA    F    21_D      F    21_F     4.307     0    0.565   0.936     9.396   39.405   21.688
LGA    D    22_D      D    22_F     2.334     0    0.568   1.072     8.302   77.381   47.500
LGA    L    23_D      L    23_F     0.669     0    0.128   1.356     4.201   90.476   75.238
LGA    A    24_D      A    24_F     1.897     0    0.034   0.042     2.676   72.976   69.810
LGA    S    25_D      S    25_F     2.261     0    0.203   0.732     3.280   75.119   70.556
LGA    W    26_D      W    26_F     1.188     0    0.026   0.897     4.411   85.952   69.524
LGA    I    27_D      I    27_F     0.511     0    0.033   1.115     2.974   95.238   80.357
LGA    K    28_D      K    28_F     0.547     0    0.056   1.003     5.105   95.238   76.243
LGA    Y    29_D      Y    29_F     0.352     0    0.065   0.408     3.271   97.619   78.135
LGA    I    30_D      I    30_F     0.638     0    0.044   1.580     4.927   92.857   77.024
LGA    Q    31_D      Q    31_F     0.988     0    0.067   1.245     6.066   88.214   67.196
LGA    R    32_D      R    32_F     1.080     0    0.315   1.418     8.602   83.690   57.100

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       25     100    100  100.00     223    223  100.00                26
SUMMARY(RMSD_GDC):     4.741          4.527                  6.249           53.539   41.587

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   29   26    4.0     18    2.36    62.500    56.228     0.731

LGA_LOCAL      RMSD:   2.362  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.307  Number of assigned atoms:   25 
Std_ASGN_ATOMS RMSD:   4.741  Standard rmsd on all 25 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.526637 * X  +  -0.073795 * Y  +   0.846881 * Z  +  15.056822
  Y_new =  -0.389006 * X  +  -0.864878 * Y  +  -0.317269 * Z  + -25.420454
  Z_new =   0.755862 * X  +  -0.496528 * Y  +   0.426770 * Z  +  54.746914 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.505388 -0.856970 -0.860808   [DEG: -143.5482  -49.1008  -49.3206 ]
ZXZ:  1.212348  1.129878  2.152009   [DEG:   69.4624   64.7373  123.3010 ]
 
# END of job
