
#######################################################
#                                                     #
#                        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   33 (  304),  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:    26       8_F - 33_F        2.41     2.41
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      11_F - 33_F        1.53     2.76
  LCS_AVERAGE:     79.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        0.94     3.18
  LCS_AVERAGE:     73.37

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   26      0    3    3    3    3    3    4    8   10   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     Q     9_D     Q     9_F      3    4   26      3    3    4    5    5   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K    10_D     K    10_F      3    4   26      3    4    4    5    5    6    8   16   17   18   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L    11_D     L    11_F      3   23   26      3    4    4    5    9   12   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     N    12_D     N    12_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     S    13_D     S    13_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     W    14_D     W    14_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D    15_D     D    15_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V    16_D     V    16_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     F    17_D     F    17_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G    18_D     G    18_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     N    19_D     N    19_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     W    20_D     W    20_F     22   23   26      3   14   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     F    21_D     F    21_F     22   23   26      3    5   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D    22_D     D    22_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L    23_D     L    23_F     22   23   26      3   11   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     A    24_D     A    24_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     S    25_D     S    25_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     W    26_D     W    26_F     22   23   26      7   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     I    27_D     I    27_F     22   23   26      8   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K    28_D     K    28_F     22   23   26      7   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     Y    29_D     Y    29_F     22   23   26      7   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     I    30_D     I    30_F     22   23   26      7   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     Q    31_D     Q    31_F     22   23   26      7   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     R    32_D     R    32_F     22   23   26      7   17   20   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     R    33_D     R    33_F     22   23   26      3   11   12   22   22   22   24   24   24   25   26   26   26   26   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  84.42  (  73.37   79.88  100.00 )

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     17     20     22     22     22     24     24     24     25     26     26     26     26     26     26     26     26     26     26 
GDT PERCENT_AT  30.77  65.38  76.92  84.62  84.62  84.62  92.31  92.31  92.31  96.15 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.63   0.80   0.94   0.94   0.94   1.76   1.76   1.76   2.07   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41
GDT RMS_ALL_AT   3.73   3.24   3.24   3.18   3.18   3.18   2.52   2.52   2.52   2.47   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F     5.904     0    0.273   0.253     9.159   20.595   16.667
LGA    Q     9_D      Q     9_F     3.981     0    0.580   0.518     7.183   29.524   50.159
LGA    K    10_D      K    10_F     7.510     0    0.039   0.645    18.466   14.643    6.561
LGA    L    11_D      L    11_F     4.689     0    0.578   1.367     9.523   37.976   23.690
LGA    N    12_D      N    12_F     2.396     0    0.577   0.550     8.057   75.238   47.500
LGA    S    13_D      S    13_F     1.671     0    0.025   0.616     2.249   77.143   74.365
LGA    W    14_D      W    14_F     1.325     0    0.091   1.632     7.774   85.952   59.762
LGA    D    15_D      D    15_F     1.117     0    0.042   0.128     2.320   85.952   80.536
LGA    V    16_D      V    16_F     0.955     0    0.037   0.066     1.613   88.214   84.082
LGA    F    17_D      F    17_F     0.968     0    0.022   0.174     2.246   90.476   78.571
LGA    G    18_D      G    18_F     0.635     0    0.060   0.060     0.862   92.857   92.857
LGA    N    19_D      N    19_F     1.071     0    0.150   0.295     2.276   81.548   74.167
LGA    W    20_D      W    20_F     1.471     0    0.000   0.081     3.712   75.119   64.864
LGA    F    21_D      F    21_F     1.940     0    0.126   1.293     4.151   79.405   65.714
LGA    D    22_D      D    22_F     0.422     0    0.119   0.166     1.039   95.238   91.726
LGA    L    23_D      L    23_F     1.589     0    0.105   0.887     4.263   81.548   67.857
LGA    A    24_D      A    24_F     1.018     0    0.018   0.018     1.199   85.952   85.048
LGA    S    25_D      S    25_F     0.543     0    0.069   0.677     1.671   92.857   89.127
LGA    W    26_D      W    26_F     0.932     0    0.030   1.512     4.129   88.214   71.531
LGA    I    27_D      I    27_F     1.360     0    0.021   0.103     2.471   83.690   75.238
LGA    K    28_D      K    28_F     0.527     0    0.062   0.654     3.478   95.238   78.677
LGA    Y    29_D      Y    29_F     1.080     0    0.021   0.363     4.214   83.690   64.643
LGA    I    30_D      I    30_F     1.555     0    0.061   0.684     5.212   77.143   65.179
LGA    Q    31_D      Q    31_F     0.888     0    0.065   0.825     5.823   90.476   67.989
LGA    R    32_D      R    32_F     0.880     0    0.453   0.981     1.977   88.452   81.688
LGA    R    33_D      R    33_F     1.845     0    0.200   1.297     8.609   59.762   43.160

# 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):     2.410          2.321                  3.695           75.266   65.437

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   26    4.0     24    1.76    85.577    86.097     1.291

LGA_LOCAL      RMSD:   1.759  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.523  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   2.410  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.414916 * X  +   0.073765 * Y  +  -0.906865 * Z  +  63.094822
  Y_new =   0.482908 * X  +   0.826885 * Y  +   0.288204 * Z  + -247.557724
  Z_new =   0.771132 * X  +  -0.557512 * Y  +   0.307466 * Z  + -104.628151 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.860984 -0.880617 -1.066805   [DEG:   49.3307  -50.4557  -61.1234 ]
ZXZ: -1.878504  1.258268  2.196779   [DEG: -107.6304   72.0934  125.8661 ]
 
# END of job
