
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.55     1.55
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.55     1.55
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       3_B - 39_B        0.95     1.56
  LCS_AVERAGE:     84.53

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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_B     A     2_B      3   41   41      3    3    6    7   13   13   16   37   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S     3_B     S     3_B     37   41   41      4   22   32   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B     37   41   41      6   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     37   41   41      5   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     37   41   41      6   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     37   41   41     14   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     37   41   41     14   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     37   41   41     14   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     37   41   41      9   23   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     37   41   41      9   20   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     37   41   41     12   18   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     37   41   41     12   16   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     37   41   41     12   18   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     37   41   41     14   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     37   41   41     14   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     37   41   41     12   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     37   41   41     14   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     37   41   41     15   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     37   41   41     18   29   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     37   41   41     12   27   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     37   41   41      4   15   28   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     23   41   41      4    6   16   21   30   38   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     23   41   41      8   16   34   37   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   41   41      3    3    3    5   36   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  94.84  (  84.53  100.00  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     18     29     34     37     38     39     40     40     40     40     41     41     41     41     41     41     41     41     41     41 
GDT PERCENT_AT  43.90  70.73  82.93  90.24  92.68  95.12  97.56  97.56  97.56  97.56 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.58   0.79   0.94   0.99   1.11   1.26   1.26   1.26   1.26   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55
GDT RMS_ALL_AT   1.65   1.57   1.56   1.57   1.56   1.56   1.57   1.57   1.57   1.57   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     6.067     0    0.706   0.692     6.436   24.405   22.952
LGA    S     3_B      S     3_B     2.128     0    0.473   0.698     2.460   70.952   70.238
LGA    Q     4_B      Q     4_B     1.117     0    0.008   0.239     2.000   83.690   78.677
LGA    R     5_B      R     5_B     0.675     0    0.092   0.385     2.446   90.476   80.996
LGA    L     6_B      L     6_B     0.798     0    0.062   0.157     1.616   88.214   83.750
LGA    F     7_B      F     7_B     0.687     0    0.024   0.143     0.826   90.476   93.939
LGA    V     8_B      V     8_B     0.874     0    0.049   1.142     2.504   90.476   80.748
LGA    L     9_B      L     9_B     0.489     0    0.021   0.136     0.790   92.857   91.667
LGA    D    10_B      D    10_B     0.520     0    0.040   0.492     1.640   92.857   88.333
LGA    N    11_B      N    11_B     0.079     0    0.073   0.853     2.211   97.619   88.810
LGA    E    12_B      E    12_B     0.555     0    0.036   1.172     6.531   92.857   68.095
LGA    R    13_B      R    13_B     0.740     0    0.047   1.138     3.737   90.476   74.113
LGA    Y    14_B      Y    14_B     0.275     0    0.054   0.118     0.913  100.000   97.619
LGA    D    15_B      D    15_B     0.121     0    0.024   0.453     1.271  100.000   94.167
LGA    S    16_B      S    16_B     0.456     0    0.016   0.768     2.339   97.619   90.952
LGA    F    17_B      F    17_B     0.294     0    0.019   0.212     0.636  100.000   98.268
LGA    I    18_B      I    18_B     0.194     0    0.025   0.103     0.299  100.000  100.000
LGA    T    19_B      T    19_B     0.312     0    0.023   0.238     1.043  100.000   97.347
LGA    Q    20_B      Q    20_B     0.337     0    0.028   0.902     2.914  100.000   89.101
LGA    L    21_B      L    21_B     0.520     0    0.015   1.306     2.791   95.238   85.476
LGA    E    22_B      E    22_B     0.589     0    0.021   0.734     2.022   92.857   82.804
LGA    A    23_B      A    23_B     0.476     0    0.082   0.099     0.604   95.238   94.286
LGA    P    24_B      P    24_B     0.890     0    0.041   0.047     1.031   90.476   87.891
LGA    V    25_B      V    25_B     1.347     0    0.096   1.293     2.737   81.429   74.354
LGA    Q    26_B      Q    26_B     1.523     0    0.032   0.651     2.835   77.143   70.370
LGA    N    27_B      N    27_B     1.841     0    0.059   0.084     1.867   72.857   72.857
LGA    A    28_B      A    28_B     1.708     0    0.106   0.119     1.883   79.405   78.095
LGA    E    29_B      E    29_B     1.579     0    0.100   0.599     3.257   79.405   68.836
LGA    G    30_B      G    30_B     1.014     0    0.108   0.108     1.260   85.952   85.952
LGA    R    31_B      R    31_B     0.880     0    0.037   1.001     4.451   90.476   77.922
LGA    E    32_B      E    32_B     0.756     0    0.100   0.766     3.578   92.857   80.000
LGA    R    33_B      R    33_B     0.611     0    0.047   1.061     2.465   92.857   85.022
LGA    L    34_B      L    34_B     0.503     0    0.016   0.083     1.027   92.857   90.536
LGA    M    35_B      M    35_B     0.452     0    0.027   0.932     3.506   95.238   88.155
LGA    A    36_B      A    36_B     0.688     0    0.028   0.031     0.940   90.476   90.476
LGA    V    37_B      V    37_B     0.769     0    0.043   0.077     1.071   88.214   89.184
LGA    K    38_B      K    38_B     1.448     4    0.114   0.130     2.781   73.214   39.735
LGA    P    39_B      P    39_B     1.866     0    0.086   0.340     2.297   70.952   74.286
LGA    E    40_B      E    40_B     3.793     0    0.386   0.313     9.248   53.810   28.995
LGA    W    41_B      W    41_B     1.901     0    0.390   0.864     3.640   59.524   59.626
LGA    K    42_B      K    42_B     3.341     0    0.151   0.980     8.183   57.262   32.804

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     1.554          1.465                  2.094           85.627   78.718

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     40    1.26    89.634    94.459     2.937

LGA_LOCAL      RMSD:   1.262  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.566  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   1.554  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.276187 * X  +   0.012740 * Y  +   0.961019 * Z  +  18.993347
  Y_new =   0.123345 * X  +   0.992113 * Y  +   0.022296 * Z  +  -7.847019
  Z_new =  -0.953156 * X  +   0.124695 * Y  +  -0.275580 * Z  +  34.031479 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.721570  1.263504  2.716678   [DEG:  155.9345   72.3935  155.6542 ]
ZXZ:  1.593992  1.849990 -1.440712   [DEG:   91.3290  105.9966  -82.5467 ]
 
# END of job
