
#######################################################
#                                                     #
#                        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        3.44     3.44
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.83     3.78
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.68     4.11
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.41     4.29
  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    9   11   13   14   16   21   23   25   30   36   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   15   20   26   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    7    7   31   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3   33   37      3    3    3    4    7   10   16   25   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    3   10   23   29   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     24   31   31   31   31   31   31   32   32   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     22   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     22   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     22   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     25   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    9   14   32   32   32   33   35   35   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  84.71  (  71.51   82.62  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     25     31     31     31     31     31     31     32     33     34     35     35     35     35     35     36     36     36     36     36 
GDT PERCENT_AT  67.57  83.78  83.78  83.78  83.78  83.78  83.78  86.49  89.19  91.89  94.59  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.32   0.41   0.41   0.41   0.41   0.41   0.41   1.17   2.07   2.10   2.52   2.52   2.52   2.40   2.40   2.78   2.78   2.78   2.78   2.78
GDT RMS_ALL_AT   4.28   4.29   4.29   4.29   4.29   4.29   4.29   4.09   3.58   3.63   3.51   3.51   3.51   3.65   3.65   3.51   3.51   3.51   3.51   3.51

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  D     9_C      D     9_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    16.110     0    0.408   0.388    17.660    0.000    0.000
LGA    E     3_C      E     3_B    10.743     0    0.620   1.026    12.449    0.714    0.635
LGA    A     4_C      A     4_B     8.221     0    0.592   0.572     9.272    3.452    3.048
LGA    E     5_C      E     5_B     8.774     0    0.619   1.006    10.427    5.714    2.857
LGA    Q     6_C      Q     6_B     5.867     0    0.596   1.301    13.749   26.548   13.439
LGA    E     7_C      E     7_B     1.256     0    0.606   0.724     8.784   85.952   49.365
LGA    K     8_C      K     8_B     0.774     0    0.071   1.263     4.622   88.214   71.111
LGA    D     9_C      D     9_B     0.867     0    0.047   0.939     3.515   90.476   77.202
LGA    Q    10_C      Q    10_B     0.630     0    0.037   0.279     1.209   90.476   89.471
LGA    L    11_C      L    11_B     0.915     0    0.014   0.071     1.066   90.476   85.952
LGA    R    12_C      R    12_B     0.772     0    0.043   1.430     7.321   90.476   64.762
LGA    T    13_C      T    13_B     0.348     0    0.025   0.990     2.446  100.000   91.088
LGA    Q    14_C      Q    14_B     0.514     0    0.016   0.638     2.752   97.619   85.132
LGA    V    15_C      V    15_B     0.621     0    0.015   0.048     0.939   95.238   93.197
LGA    V    16_C      V    16_B     0.507     0    0.024   0.083     0.706   97.619   94.558
LGA    R    17_C      R    17_B     0.273     0    0.023   1.725     7.707  100.000   67.489
LGA    L    18_C      L    18_B     0.247     0    0.016   0.104     0.379  100.000  100.000
LGA    Q    19_C      Q    19_B     0.276     0    0.020   0.185     0.839  100.000   98.942
LGA    A    20_C      A    20_B     0.275     0    0.019   0.019     0.365  100.000  100.000
LGA    E    21_C      E    21_B     0.276     0    0.015   0.114     0.840  100.000   96.825
LGA    K    22_C      K    22_B     0.265     0    0.034   0.071     0.626  100.000   97.884
LGA    A    23_C      A    23_B     0.197     0    0.000   0.008     0.286  100.000  100.000
LGA    D    24_C      D    24_B     0.298     0    0.010   0.203     1.344  100.000   95.298
LGA    L    25_C      L    25_B     0.145     0    0.011   0.027     0.531  100.000   97.619
LGA    L    26_C      L    26_B     0.458     0    0.037   0.044     0.659   95.238   92.857
LGA    G    27_C      G    27_B     0.704     0    0.084   0.084     0.704   95.238   95.238
LGA    I    28_C      I    28_B     0.295     0    0.016   0.079     0.865  100.000   97.619
LGA    V    29_C      V    29_B     0.356     0    0.022   0.052     0.550  100.000   98.639
LGA    S    30_C      S    30_B     0.636     0    0.028   0.093     0.968   90.476   90.476
LGA    E    31_C      E    31_B     0.678     0    0.035   1.031     6.353   95.238   64.127
LGA    L    32_C      L    32_B     0.323     0    0.005   0.036     0.917  100.000   95.238
LGA    Q    33_C      Q    33_B     0.598     0    0.043   1.069     3.859   97.619   85.450
LGA    L    34_C      L    34_B     0.387     0    0.047   0.181     1.199  100.000   94.107
LGA    K    35_C      K    35_B     0.205     0    0.036   0.544     2.546   97.619   92.116
LGA    L    36_C      L    36_B     0.616     0    0.108   0.130     0.985   95.238   92.857
LGA    N    37_C      N    37_B     0.416     0    0.443   0.857     6.711   74.405   54.405
LGA    S    38_C      S    38_B     7.386     0    0.517   0.806    11.025   10.833    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):     3.436          3.366                  3.895           81.483   73.965

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     32    1.17    87.838    86.503     2.520

LGA_LOCAL      RMSD:   1.170  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.086  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.436  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.505840 * X  +   0.739646 * Y  +   0.443902 * Z  + -34.128971
  Y_new =  -0.089594 * X  +  -0.556858 * Y  +   0.825762 * Z  +  47.395279
  Z_new =   0.857962 * X  +   0.377933 * Y  +   0.347949 * Z  + -40.830299 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.966292 -1.031289  0.826681   [DEG: -169.9560  -59.0885   47.3653 ]
ZXZ:  2.648345  1.215414  1.155870   [DEG:  151.7390   69.6381   66.2265 ]
 
# END of job
