
#######################################################
#                                                     #
#                        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        3.39     3.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.81     3.73
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.67     4.06
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.40     4.24
  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   17   21   23   27   32   36   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   16   22   29   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    6    8   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    6   10   17   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    4    9   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     26   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     23   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     26   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     26   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     26   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     23   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     26   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     26   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     26   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     26   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     23   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     26   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    9   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     26     31     31     31     31     31     31     32     33     34     35     35     35     35     35     36     36     36     36     36 
GDT PERCENT_AT  70.27  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   0.40   0.40   0.40   0.40   0.40   0.40   1.15   2.05   2.09   2.49   2.49   2.49   2.39   2.39   2.75   2.75   2.75   2.75   2.75
GDT RMS_ALL_AT   4.24   4.24   4.24   4.24   4.24   4.24   4.24   4.03   3.54   3.58   3.46   3.46   3.46   3.61   3.61   3.47   3.47   3.47   3.47   3.47

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  E     7_C      E     7_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    15.827     0    0.405   0.386    17.346    0.000    0.000
LGA    E     3_C      E     3_B    10.499     0    0.638   1.043    12.180    1.071    0.847
LGA    A     4_C      A     4_B     8.222     0    0.592   0.570     9.240    3.452    3.048
LGA    E     5_C      E     5_B     8.739     0    0.609   0.977    10.425    6.905    3.280
LGA    Q     6_C      Q     6_B     5.791     0    0.596   1.299    13.661   29.643   14.815
LGA    E     7_C      E     7_B     1.297     0    0.591   0.967     9.952   85.952   46.296
LGA    K     8_C      K     8_B     0.754     0    0.085   1.278     4.869   90.476   71.429
LGA    D     9_C      D     9_B     0.793     0    0.049   0.190     0.987   90.476   90.476
LGA    Q    10_C      Q    10_B     0.565     0    0.039   0.292     1.121   92.857   90.529
LGA    L    11_C      L    11_B     0.893     0    0.012   0.062     1.084   90.476   85.952
LGA    R    12_C      R    12_B     0.834     0    0.012   0.463     3.878   90.476   74.719
LGA    T    13_C      T    13_B     0.334     0    0.023   0.985     2.348  100.000   91.088
LGA    Q    14_C      Q    14_B     0.459     0    0.032   1.212     5.149  100.000   72.910
LGA    V    15_C      V    15_B     0.491     0    0.012   0.039     0.635  100.000   95.918
LGA    V    16_C      V    16_B     0.408     0    0.019   0.081     0.468  100.000  100.000
LGA    R    17_C      R    17_B     0.333     0    0.061   1.804    10.501  100.000   56.147
LGA    L    18_C      L    18_B     0.316     0    0.018   0.115     0.408  100.000  100.000
LGA    Q    19_C      Q    19_B     0.279     0    0.014   0.176     0.777  100.000   98.942
LGA    A    20_C      A    20_B     0.286     0    0.019   0.021     0.383  100.000  100.000
LGA    E    21_C      E    21_B     0.253     0    0.018   0.062     0.591  100.000   97.884
LGA    K    22_C      K    22_B     0.249     0    0.035   0.073     0.602  100.000   97.884
LGA    A    23_C      A    23_B     0.204     0    0.000   0.009     0.263  100.000  100.000
LGA    D    24_C      D    24_B     0.256     0    0.009   0.204     1.306  100.000   95.298
LGA    L    25_C      L    25_B     0.133     0    0.008   0.028     0.496  100.000  100.000
LGA    L    26_C      L    26_B     0.459     0    0.038   0.045     0.634   95.238   95.238
LGA    G    27_C      G    27_B     0.690     0    0.083   0.083     0.690   95.238   95.238
LGA    I    28_C      I    28_B     0.301     0    0.016   0.079     0.809  100.000   97.619
LGA    V    29_C      V    29_B     0.347     0    0.021   0.051     0.507  100.000   98.639
LGA    S    30_C      S    30_B     0.621     0    0.029   0.096     0.945   90.476   90.476
LGA    E    31_C      E    31_B     0.674     0    0.035   1.044     6.359   95.238   64.127
LGA    L    32_C      L    32_B     0.316     0    0.006   0.036     0.875  100.000   96.429
LGA    Q    33_C      Q    33_B     0.583     0    0.042   1.069     3.845   97.619   85.450
LGA    L    34_C      L    34_B     0.375     0    0.046   0.181     1.184  100.000   94.107
LGA    K    35_C      K    35_B     0.214     0    0.035   0.555     2.656   97.619   92.116
LGA    L    36_C      L    36_B     0.613     0    0.109   0.131     0.976   95.238   92.857
LGA    N    37_C      N    37_B     0.407     0    0.441   0.855     6.692   74.405   54.405
LGA    S    38_C      S    38_B     7.387     0    0.512   0.802    11.024   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):     3.394          3.324                  4.003           81.992   74.375

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     32    1.15    87.838    86.503     2.555

LGA_LOCAL      RMSD:   1.152  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.033  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.394  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.848904 * X  +  -0.022396 * Y  +   0.528073 * Z  + -35.108650
  Y_new =   0.504706 * X  +  -0.262341 * Y  +  -0.822466 * Z  +  44.285599
  Z_new =   0.156955 * X  +   0.964715 * Y  +  -0.211398 * Z  + -40.112869 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.536394 -0.157607  1.786517   [DEG:   30.7331   -9.0302  102.3599 ]
ZXZ:  0.570774  1.783802  0.161283   [DEG:   32.7029  102.2043    9.2408 ]
 
# END of job
