
#######################################################
#                                                     #
#                        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:    22      12_F - 33_F        4.85     7.48
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.74    12.18
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.61    12.57
  LCS_AVERAGE:     39.79

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   20      0    3    3    3    3    3    4    8   14   15   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   20      3    3    5    5    6   10   13   13   14   15   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    5    5    6    6    8   10   11   13   15   16   19   20   22   22   24   25   25   26 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    5    5    9   11   13   13   14   15   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    9    9   11   11   11   13   13   14   15   16   18   19   20   22   22   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    9    9   11   11   11   13   13   15   16   16   19   19   20   22   22   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    9    9   11   11   11   13   13   14   15   16   18   19   20   22   22   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    9    9   11   11   11   13   13   14   15   16   19   19   20   22   22   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    9    9   11   11   11   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    9    9   11   11   11   13   13   15   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    9    9   11   11   11   13   13   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    9    9   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    9    9   11   11   11   13   14   15   15   16   18   19   20   22   22   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    3    9   11   11   11   13   15   16   16   17   19   19   20   21   22   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   12   12   13   13   14   15   16   16   17   19   19   20   21   22   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      6   11   12   12   13   13   14   15   16   16   17   19   19   20   21   22   23   23   24   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      8   11   12   12   13   13   14   15   16   16   17   19   19   20   22   22   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   12   12   13   13   14   15   16   16   17   19   19   20   21   22   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.87  (  39.79   44.38   83.43 )

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      9     11     12     12     13     13     14     15     16     16     17     19     19     20     22     22     24     25     25     26 
GDT PERCENT_AT  34.62  42.31  46.15  46.15  50.00  50.00  53.85  57.69  61.54  61.54  65.38  73.08  73.08  76.92  84.62  84.62  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.27   0.38   0.61   0.61   0.97   0.97   1.78   2.21   2.65   2.65   3.12   3.94   3.94   4.31   5.19   5.05   5.70   5.85   5.85   6.10
GDT RMS_ALL_AT  12.39  12.62  12.57  12.57  11.67  11.67  10.20  10.43   9.75   9.75   9.43   8.07   8.07   7.46   6.41   6.65   6.12   6.15   6.15   6.10

# Checking swapping
#   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    27.061     0    0.278   0.261    30.009    0.000    0.000
LGA    Q     9_D      Q     9_F    20.657     0    0.573   0.491    23.264    0.000    0.000
LGA    K    10_D      K    10_F    20.350     0    0.047   0.640    25.900    0.000    0.000
LGA    L    11_D      L    11_F    17.550     0    0.602   0.633    18.706    0.000    0.000
LGA    N    12_D      N    12_F    14.500     0    0.565   0.558    18.555    0.000    0.000
LGA    S    13_D      S    13_F    12.672     0    0.030   0.078    14.859    0.000    0.000
LGA    W    14_D      W    14_F    14.823     0    0.050   1.502    24.285    0.000    0.000
LGA    D    15_D      D    15_F    10.679     0    0.010   0.168    16.097    6.071    3.036
LGA    V    16_D      V    16_F     4.361     0    0.000   0.041     6.795   30.000   33.946
LGA    F    17_D      F    17_F     9.053     0    0.014   1.221    17.848    5.714    2.078
LGA    G    18_D      G    18_F     6.818     0    0.192   0.192     7.531   28.452   28.452
LGA    N    19_D      N    19_F     1.638     0    0.242   0.993     6.742   54.643   42.083
LGA    W    20_D      W    20_F     6.452     0    0.159   1.299    12.338   19.643    6.361
LGA    F    21_D      F    21_F     4.796     0    0.558   0.933     9.913   42.500   20.866
LGA    D    22_D      D    22_F     2.495     0    0.572   1.350     7.727   66.786   42.500
LGA    L    23_D      L    23_F     2.161     0    0.112   0.908     3.109   68.810   65.000
LGA    A    24_D      A    24_F     1.950     0    0.026   0.029     2.130   72.976   71.333
LGA    S    25_D      S    25_F     1.743     0    0.150   0.719     2.408   79.405   77.302
LGA    W    26_D      W    26_F     1.349     0    0.028   0.226     3.105   85.952   71.054
LGA    I    27_D      I    27_F     0.437     0    0.032   0.099     0.880   97.619   96.429
LGA    K    28_D      K    28_F     0.441     0    0.080   0.617     5.247   97.619   72.540
LGA    Y    29_D      Y    29_F     0.260     0    0.054   0.453     3.150   95.238   78.651
LGA    I    30_D      I    30_F     1.064     0    0.073   0.101     1.936   83.690   79.345
LGA    Q    31_D      Q    31_F     1.806     0    0.027   1.240     7.036   72.976   54.921
LGA    R    32_D      R    32_F     1.376     0    0.473   1.240     2.615   77.262   72.381
LGA    R    33_D      R    33_F     1.449     0    0.587   1.239     5.851   79.286   55.584

# 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):     6.103          5.920                  8.075           44.794   37.456

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.21    57.692    54.482     0.650

LGA_LOCAL      RMSD:   2.208  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.431  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.103  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.797305 * X  +   0.064078 * Y  +   0.600165 * Z  +  24.780724
  Y_new =  -0.147034 * X  +   0.985013 * Y  +   0.090164 * Z  + -82.412003
  Z_new =  -0.585393 * X  +  -0.160133 * Y  +   0.794778 * Z  +   6.621777 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.182365  0.625365 -0.198819   [DEG:  -10.4487   35.8308  -11.3915 ]
ZXZ:  1.719913  0.652154 -1.837812   [DEG:   98.5438   37.3657 -105.2989 ]
 
# END of job
