
#######################################################
#                                                     #
#                        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   38 (  302),  selected   37 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        3.70     3.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.83     4.46
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.42     4.69
  LCS_AVERAGE:     71.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     A     2_C     A     2_B      3    3   37      0    3    3    3    3    4    4    8    9    9   11   13   14   16   21   22   24   27   31   35 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   14   19   25   29   32   35   35   35   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    6    7   30   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    6   10   15   22   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4    8   16   26   30   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     24   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     24   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     24   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     27   31   31   31   31   31   31   31   32   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    3    4    5    7    9   19   25   32   32   32   35   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  83.98  (  71.51   80.42  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     27     31     31     31     31     31     31     31     32     34     34     34     35     35     35     36     36     36     36     36 
GDT PERCENT_AT  72.97  83.78  83.78  83.78  83.78  83.78  83.78  83.78  86.49  91.89  91.89  91.89  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.35   0.42   0.42   0.42   0.42   0.42   0.42   0.42   1.32   2.31   2.31   2.31   2.76   2.76   2.60   3.02   3.02   3.02   3.02   3.02
GDT RMS_ALL_AT   4.77   4.69   4.69   4.69   4.69   4.69   4.69   4.69   4.44   3.91   3.91   3.91   3.78   3.78   3.94   3.78   3.78   3.78   3.78   3.78

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    21_C      E    21_B
#   possible swapping detected:  E    31_C      E    31_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    18.244     0    0.438   0.428    19.872    0.000    0.000
LGA    E     3_C      E     3_B    12.695     0    0.603   1.012    14.507    0.000    0.000
LGA    A     4_C      A     4_B     9.678     0    0.630   0.585    10.896    0.119    0.095
LGA    E     5_C      E     5_B    10.386     0    0.604   0.816    13.704    1.071    0.476
LGA    Q     6_C      Q     6_B     7.492     0    0.601   1.315    15.131   16.429    7.619
LGA    E     7_C      E     7_B     0.277     0    0.583   0.959     8.379   89.286   53.280
LGA    K     8_C      K     8_B     0.520     0    0.060   1.374     7.296   92.857   68.466
LGA    D     9_C      D     9_B     0.835     0    0.050   0.180     2.398   90.476   81.726
LGA    Q    10_C      Q    10_B     0.655     0    0.050   0.451     2.263   92.857   85.661
LGA    L    11_C      L    11_B     0.359     0    0.010   0.060     0.862  100.000   95.238
LGA    R    12_C      R    12_B     0.513     0    0.020   0.376     2.170   97.619   85.065
LGA    T    13_C      T    13_B     0.351     0    0.025   0.934     2.639  100.000   88.639
LGA    Q    14_C      Q    14_B     0.521     0    0.012   0.957     3.939   97.619   78.995
LGA    V    15_C      V    15_B     0.445     0    0.024   0.056     0.815  100.000   95.918
LGA    V    16_C      V    16_B     0.288     0    0.017   0.096     0.612  100.000   98.639
LGA    R    17_C      R    17_B     0.130     0    0.051   1.946     9.732  100.000   61.255
LGA    L    18_C      L    18_B     0.243     0    0.016   0.075     0.672  100.000   97.619
LGA    Q    19_C      Q    19_B     0.260     0    0.017   0.211     0.806  100.000   97.884
LGA    A    20_C      A    20_B     0.226     0    0.049   0.058     0.322  100.000  100.000
LGA    E    21_C      E    21_B     0.290     0    0.013   0.133     0.888  100.000   96.825
LGA    K    22_C      K    22_B     0.515     0    0.033   0.153     1.023   92.857   90.529
LGA    A    23_C      A    23_B     0.482     0    0.011   0.021     0.530  100.000   98.095
LGA    D    24_C      D    24_B     0.323     0    0.050   0.757     2.862  100.000   85.893
LGA    L    25_C      L    25_B     0.354     0    0.016   0.063     0.546  100.000   98.810
LGA    L    26_C      L    26_B     0.286     0    0.027   0.108     0.678  100.000   96.429
LGA    G    27_C      G    27_B     0.403     0    0.085   0.085     0.403  100.000  100.000
LGA    I    28_C      I    28_B     0.373     0    0.019   0.103     0.498  100.000  100.000
LGA    V    29_C      V    29_B     0.171     0    0.028   0.053     0.364  100.000  100.000
LGA    S    30_C      S    30_B     0.245     0    0.026   0.052     0.317  100.000  100.000
LGA    E    31_C      E    31_B     0.362     0    0.019   0.900     4.831  100.000   76.349
LGA    L    32_C      L    32_B     0.216     0    0.000   0.061     0.633  100.000   98.810
LGA    Q    33_C      Q    33_B     0.508     0    0.043   1.055     3.181   92.857   84.074
LGA    L    34_C      L    34_B     0.544     0    0.042   0.217     1.064   92.857   90.536
LGA    K    35_C      K    35_B     0.376     0    0.026   0.496     2.295   97.619   92.963
LGA    L    36_C      L    36_B     0.499     0    0.044   0.077     0.524   97.619   98.810
LGA    N    37_C      N    37_B     0.506     0    0.282   0.820     6.800   70.357   50.952
LGA    S    38_C      S    38_B     7.502     0    0.041   0.189     9.574   11.071    7.698

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     291    291  100.00                37
SUMMARY(RMSD_GDC):     3.705          3.605                  4.214           81.988   74.685

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.42    87.162    85.480     5.993

LGA_LOCAL      RMSD:   0.417  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.689  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.705  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.870370 * X  +   0.340285 * Y  +   0.355897 * Z  + -11.965267
  Y_new =  -0.003788 * X  +   0.718134 * Y  +  -0.695895 * Z  +  29.660246
  Z_new =  -0.492384 * X  +  -0.607034 * Y  +  -0.623753 * Z  + -41.066216 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.137241  0.514827 -2.369778   [DEG: -179.7507   29.4974 -135.7783 ]
ZXZ:  0.472745  2.244332 -2.460101   [DEG:   27.0863  128.5907 -140.9534 ]
 
# END of job
