
#######################################################
#                                                     #
#                        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        3.80     3.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.88     4.57
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.48     4.79
  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    7    9   10   11   13   14   16   21   23   24   27   31   34 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   15   19   24   28   32   35   35   35   35   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    5    6    8   22   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    5    8   12   20   26   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    6    8   16   23   30   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     11   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    7    9   19   25   32   32   32   34   35   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     23     31     31     31     31     31     31     31     33     34     34     34     35     35     35     35     36     36     36     36 
GDT PERCENT_AT  62.16  83.78  83.78  83.78  83.78  83.78  83.78  83.78  89.19  91.89  91.89  91.89  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.31   0.48   0.48   0.48   0.48   0.48   0.48   0.48   2.00   2.41   2.41   2.41   2.85   2.85   2.85   2.70   3.11   3.11   3.11   3.11
GDT RMS_ALL_AT   4.76   4.79   4.79   4.79   4.79   4.79   4.79   4.79   4.19   4.00   4.00   4.00   3.87   3.87   3.87   4.03   3.88   3.88   3.88   3.88

# 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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    18.501     0    0.449   0.441    19.995    0.000    0.000
LGA    E     3_C      E     3_B    12.871     0    0.606   1.022    14.729    0.000    0.000
LGA    A     4_C      A     4_B    10.095     0    0.631   0.585    11.260    0.000    0.000
LGA    E     5_C      E     5_B    10.760     0    0.603   0.764    14.083    0.714    0.317
LGA    Q     6_C      Q     6_B     7.635     0    0.606   1.080    13.087   14.048    6.614
LGA    E     7_C      E     7_B     0.430     0    0.589   0.962     8.396   84.524   51.164
LGA    K     8_C      K     8_B     0.717     0    0.062   1.363     7.412   92.857   66.720
LGA    D     9_C      D     9_B     0.822     0    0.029   0.192     2.452   90.476   80.714
LGA    Q    10_C      Q    10_B     0.667     0    0.049   0.388     2.078   92.857   85.661
LGA    L    11_C      L    11_B     0.280     0    0.016   0.067     0.631  100.000   97.619
LGA    R    12_C      R    12_B     0.416     0    0.024   0.357     1.599  100.000   89.091
LGA    T    13_C      T    13_B     0.351     0    0.018   0.953     2.704  100.000   88.639
LGA    Q    14_C      Q    14_B     0.455     0    0.013   0.814     3.974  100.000   80.952
LGA    V    15_C      V    15_B     0.441     0    0.024   0.061     0.733  100.000   95.918
LGA    V    16_C      V    16_B     0.343     0    0.018   0.111     0.690  100.000   98.639
LGA    R    17_C      R    17_B     0.108     0    0.048   1.952     9.923  100.000   59.827
LGA    L    18_C      L    18_B     0.329     0    0.018   0.073     0.672  100.000   96.429
LGA    Q    19_C      Q    19_B     0.416     0    0.020   0.171     0.858  100.000   95.767
LGA    A    20_C      A    20_B     0.384     0    0.070   0.079     0.574   97.619   98.095
LGA    E    21_C      E    21_B     0.386     0    0.017   0.114     0.926   95.238   94.709
LGA    K    22_C      K    22_B     0.643     0    0.031   0.115     1.177   90.476   89.471
LGA    A    23_C      A    23_B     0.645     0    0.025   0.034     0.702   90.476   90.476
LGA    D    24_C      D    24_B     0.419     0    0.027   0.242     1.219  100.000   96.488
LGA    L    25_C      L    25_B     0.478     0    0.013   0.068     0.681   97.619   94.048
LGA    L    26_C      L    26_B     0.413     0    0.041   0.095     0.943  100.000   95.238
LGA    G    27_C      G    27_B     0.455     0    0.076   0.076     0.464  100.000  100.000
LGA    I    28_C      I    28_B     0.406     0    0.019   0.087     0.560  100.000   97.619
LGA    V    29_C      V    29_B     0.298     0    0.032   0.053     0.592  100.000   98.639
LGA    S    30_C      S    30_B     0.217     0    0.037   0.580     1.810  100.000   95.476
LGA    E    31_C      E    31_B     0.317     0    0.022   1.065     5.508  100.000   72.751
LGA    L    32_C      L    32_B     0.167     0    0.013   0.078     0.631  100.000   98.810
LGA    Q    33_C      Q    33_B     0.484     0    0.032   1.046     2.811   95.238   87.989
LGA    L    34_C      L    34_B     0.687     0    0.061   0.209     1.036   90.476   89.345
LGA    K    35_C      K    35_B     0.623     0    0.030   0.505     2.566   90.476   85.767
LGA    L    36_C      L    36_B     0.560     0    0.041   0.081     0.593   90.476   94.048
LGA    N    37_C      N    37_B     0.529     0    0.332   0.836     6.691   70.357   52.381
LGA    S    38_C      S    38_B     7.637     0    0.614   0.792     9.651   10.714    7.460

# 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):     3.798          3.707                  4.251           80.936   73.862

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.48    86.486    85.563     5.380

LGA_LOCAL      RMSD:   0.476  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.791  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.798  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.362488 * X  +   0.329488 * Y  +   0.871803 * Z  + -13.317421
  Y_new =   0.720778 * X  +   0.692117 * Y  +   0.038115 * Z  +  30.099667
  Z_new =  -0.590831 * X  +   0.642193 * Y  +  -0.488372 * Z  + -39.831787 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.036770  0.632089  2.220968   [DEG:  116.6983   36.2160  127.2521 ]
ZXZ:  1.614488  2.081019 -0.743767   [DEG:   92.5034  119.2336  -42.6147 ]
 
# END of job
