
#######################################################
#                                                     #
#                        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        4.77     7.21
  LCS_AVERAGE:     83.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.74    12.39
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.65    12.97
  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   19      0    3    3    3    3    3    4    7   14   16   17   18   19   19   22   22   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   19      3    3    4    6    6    8   10   13   14   16   17   18   19   19   23   23   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    4    6    6    6    7   10   11   13   15   15   17   18   19   22   23   25   25   26 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    4    6    9   11   12   13   14   16   17   18   19   20   23   23   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    8    9   11   11   11   12   13   14   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    8    9   11   11   11   12   13   14   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    8    9   11   11   11   12   13   14   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    8    9   11   11   11   12   13   14   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    8    9   11   11   11   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    8    9   11   11   11   12   13   14   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    8    9   11   11   11   12   14   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    8    9   11   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    8    9   11   11   11   12   14   15   16   17   19   20   20   22   22   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4    9   11   11   11   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   18   19   20   23   23   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   11   12   13   13   14   15   15   16   17   18   20   20   23   23   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      6   11   11   12   13   13   14   15   15   16   17   18   19   20   23   23   23   23   25   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      6   11   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    6   11   12   13   13   14   15   15   16   17   19   20   20   23   23   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.77  (  39.79   44.38   83.14 )

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     11     12     13     13     14     15     15     16     17     19     20     20     23     23     24     25     25     26 
GDT PERCENT_AT  34.62  42.31  42.31  46.15  50.00  50.00  53.85  57.69  57.69  61.54  65.38  73.08  76.92  76.92  88.46  88.46  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.24   0.41   0.41   0.65   1.08   1.08   1.81   2.30   2.30   2.71   3.21   4.28   4.39   4.39   5.26   5.26   5.57   5.81   5.80   6.05
GDT RMS_ALL_AT  12.56  12.89  12.89  12.97  11.92  11.92  11.75  10.46  12.02   9.74   9.32   6.94   6.96   6.96   6.32   6.32   6.10   6.10   6.09   6.05

# Checking swapping
#   possible swapping detected:  F    21_D      F    21_F
#   possible swapping detected:  D    22_D      D    22_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    26.409     0    0.280   0.261    28.662    0.000    0.000
LGA    Q     9_D      Q     9_F    20.490     0    0.576   0.488    22.914    0.000    0.000
LGA    K    10_D      K    10_F    20.978     0    0.049   0.636    27.305    0.000    0.000
LGA    L    11_D      L    11_F    17.799     0    0.598   0.628    19.202    0.000    0.000
LGA    N    12_D      N    12_F    14.327     0    0.573   0.561    17.753    0.000    0.000
LGA    S    13_D      S    13_F    13.188     0    0.035   0.073    15.621    0.000    0.000
LGA    W    14_D      W    14_F    15.067     0    0.061   1.492    23.989    0.000    0.000
LGA    D    15_D      D    15_F    10.703     0    0.010   0.165    15.751    6.071    3.036
LGA    V    16_D      V    16_F     4.767     0    0.000   0.053     7.023   25.000   27.075
LGA    F    17_D      F    17_F     9.301     0    0.028   1.180    18.082    5.119    1.861
LGA    G    18_D      G    18_F     6.816     0    0.209   0.209     7.637   28.452   28.452
LGA    N    19_D      N    19_F     1.631     0    0.248   0.994     6.774   54.643   43.333
LGA    W    20_D      W    20_F     6.339     0    0.156   1.306    12.257   20.595    6.565
LGA    F    21_D      F    21_F     4.480     0    0.594   1.259    11.650   45.833   20.649
LGA    D    22_D      D    22_F     2.840     0    0.572   1.353     8.129   62.976   38.690
LGA    L    23_D      L    23_F     2.191     0    0.103   1.041     4.449   68.810   64.405
LGA    A    24_D      A    24_F     1.864     0    0.023   0.026     2.039   72.976   71.333
LGA    S    25_D      S    25_F     1.866     0    0.175   0.729     2.624   77.143   74.524
LGA    W    26_D      W    26_F     1.497     0    0.049   1.273     6.149   79.286   61.667
LGA    I    27_D      I    27_F     0.556     0    0.033   0.090     0.863   95.238   95.238
LGA    K    28_D      K    28_F     0.479     0    0.096   0.613     5.314   97.619   72.540
LGA    Y    29_D      Y    29_F     0.375     0    0.037   1.236     7.392   95.238   62.817
LGA    I    30_D      I    30_F     1.189     0    0.058   0.692     3.315   81.548   73.333
LGA    Q    31_D      Q    31_F     1.983     0    0.010   1.224     7.107   72.976   54.921
LGA    R    32_D      R    32_F     1.520     0    0.489   1.235     3.132   72.976   67.229
LGA    R    33_D      R    33_F     1.823     0    0.603   0.833    11.733   75.000   35.671

# 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):     6.047          5.867                  7.570           43.750   34.744

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.30    58.654    54.280     0.626

LGA_LOCAL      RMSD:   2.298  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.465  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.047  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.014020 * X  +   0.265781 * Y  +   0.963932 * Z  +  26.302847
  Y_new =   0.407519 * X  +   0.881847 * Y  +  -0.237221 * Z  + -83.278290
  Z_new =  -0.913089 * X  +   0.389495 * Y  +  -0.120674 * Z  +   6.182128 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.605186  1.150797  1.871240   [DEG:   91.9704   65.9358  107.2142 ]
ZXZ:  1.329494  1.691765 -1.167598   [DEG:   76.1744   96.9310  -66.8985 ]
 
# END of job
