
#######################################################
#                                                     #
#                        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        3.69     3.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.80     4.44
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.46     4.67
  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    9    9   10   11   13   16   17   21   23   26   29   32   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   17   21   24   30   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    6    8   24   33   34   34   35   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   14   21   28   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    3   11   17   27   30   33   34   34   35   35   35   35   36   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   35   35   35   35   36   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   35   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   33   34   34   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   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   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   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    7    9   20   31   32   32   34   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     23     31     31     31     31     31     31     31     33     34     34     35     35     35     35     36     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  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.31   0.46   0.46   0.46   0.46   0.46   0.46   0.46   1.94   2.34   2.34   2.77   2.77   2.77   2.61   3.01   3.01   3.01   3.01   3.01
GDT RMS_ALL_AT   4.61   4.67   4.67   4.67   4.67   4.67   4.67   4.67   4.07   3.89   3.89   3.76   3.76   3.76   3.92   3.76   3.76   3.76   3.76   3.76

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  E    21_C      E    21_B
#   possible swapping detected:  D    24_C      D    24_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    18.077     0    0.418   0.404    19.606    0.000    0.000
LGA    E     3_C      E     3_B    12.555     0    0.619   1.059    14.355    0.000    0.000
LGA    A     4_C      A     4_B     9.861     0    0.600   0.580    11.061    0.119    0.095
LGA    E     5_C      E     5_B    10.466     0    0.618   1.003    12.419    0.714    0.317
LGA    Q     6_C      Q     6_B     7.393     0    0.612   1.049    12.574   16.429    7.989
LGA    E     7_C      E     7_B     0.386     0    0.603   0.954     8.634   86.905   52.011
LGA    K     8_C      K     8_B     0.599     0    0.077   1.384     7.520   95.238   68.466
LGA    D     9_C      D     9_B     0.674     0    0.036   0.182     1.642   92.857   87.202
LGA    Q    10_C      Q    10_B     0.580     0    0.021   0.330     1.806   92.857   89.577
LGA    L    11_C      L    11_B     0.343     0    0.017   0.084     0.413  100.000  100.000
LGA    R    12_C      R    12_B     0.459     0    0.004   0.186     2.008  100.000   85.974
LGA    T    13_C      T    13_B     0.398     0    0.010   0.970     2.656  100.000   88.639
LGA    Q    14_C      Q    14_B     0.550     0    0.009   0.123     1.348   97.619   90.635
LGA    V    15_C      V    15_B     0.441     0    0.018   0.046     0.708  100.000   95.918
LGA    V    16_C      V    16_B     0.362     0    0.021   0.100     0.624  100.000   98.639
LGA    R    17_C      R    17_B     0.246     0    0.022   1.664     7.238  100.000   68.139
LGA    L    18_C      L    18_B     0.309     0    0.028   0.041     0.568  100.000   97.619
LGA    Q    19_C      Q    19_B     0.417     0    0.008   0.116     0.686  100.000   98.942
LGA    A    20_C      A    20_B     0.316     0    0.007   0.008     0.327  100.000  100.000
LGA    E    21_C      E    21_B     0.253     0    0.014   0.115     0.980  100.000   96.825
LGA    K    22_C      K    22_B     0.583     0    0.005   0.085     1.014   92.857   90.529
LGA    A    23_C      A    23_B     0.635     0    0.008   0.009     0.637   90.476   90.476
LGA    D    24_C      D    24_B     0.550     0    0.009   0.235     1.413   90.476   89.345
LGA    L    25_C      L    25_B     0.451     0    0.009   0.066     0.673  100.000   97.619
LGA    L    26_C      L    26_B     0.451     0    0.041   0.074     0.760  100.000   95.238
LGA    G    27_C      G    27_B     0.519     0    0.023   0.023     0.559   95.238   95.238
LGA    I    28_C      I    28_B     0.310     0    0.023   0.085     0.736  100.000   97.619
LGA    V    29_C      V    29_B     0.252     0    0.024   0.046     0.372  100.000  100.000
LGA    S    30_C      S    30_B     0.337     0    0.014   0.031     0.531  100.000   98.413
LGA    E    31_C      E    31_B     0.317     0    0.011   1.056     5.464  100.000   72.857
LGA    L    32_C      L    32_B     0.198     0    0.010   0.094     0.792  100.000   98.810
LGA    Q    33_C      Q    33_B     0.512     0    0.019   1.049     3.079   92.857   87.090
LGA    L    34_C      L    34_B     0.632     0    0.020   0.221     1.050   90.476   89.345
LGA    K    35_C      K    35_B     0.558     0    0.019   0.577     2.733   90.476   87.884
LGA    L    36_C      L    36_B     0.584     0    0.085   0.096     0.707   90.476   92.857
LGA    N    37_C      N    37_B     0.554     0    0.348   0.856     6.890   72.024   52.500
LGA    S    38_C      S    38_B     7.283     0    0.084   0.229     9.434   14.167    9.921

# 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):     3.687          3.585                  4.051           81.142   74.939

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.46    87.162    85.706     5.501

LGA_LOCAL      RMSD:   0.464  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.666  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.687  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.084784 * X  +   0.524234 * Y  +  -0.847343 * Z  + -14.163234
  Y_new =  -0.180518 * X  +   0.844414 * Y  +   0.504360 * Z  +  32.798477
  Z_new =   0.979911 * X  +   0.110199 * Y  +   0.166227 * Z  + -39.623894 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.131703 -1.370013  0.585419   [DEG:  -64.8418  -78.4960   33.5421 ]
ZXZ: -2.107697  1.403794  1.458809   [DEG: -120.7622   80.4315   83.5836 ]
 
# END of job
