
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    43       5_B - 47_B        2.18     2.18
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       5_B - 45_B        1.84     2.26
  LCS_AVERAGE:     91.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_B - 36_B        0.95     2.64
  LONGEST_CONTINUOUS_SEGMENT:    32       6_B - 37_B        0.96     2.71
  LCS_AVERAGE:     64.31

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     32   41   43      5   17   28   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     32   41   43     18   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     32   41   43     18   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     32   41   43     18   27   29   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     32   41   43     18   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     32   41   43     18   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     32   41   43     16   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     32   41   43     19   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     32   41   43     16   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     32   41   43     10   27   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     32   41   43      7   21   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     32   41   43      7   13   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     32   41   43      7   21   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     32   41   43      7   21   30   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     32   41   43      7   13   28   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     20   41   43      7   13   20   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     20   41   43      7   13   23   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     20   41   43      6   13   23   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     19   41   43      4   11   19   36   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     19   41   43      5    9   18   35   38   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     12   41   43      4    7   11   16   37   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     10   41   43      4    6   10   12   19   39   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   41   43      4    6    8   11   19   27   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   15   43      3    3    3    3    6    6    9   14   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3   42   42   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  85.40  (  64.31   91.89  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     19     27     30     36     38     39     42     42     43     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  44.19  62.79  69.77  83.72  88.37  90.70  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.51   0.88   1.13   1.25   1.42   1.94   1.94   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18
GDT RMS_ALL_AT   2.64   2.60   2.67   2.87   2.72   2.54   2.22   2.22   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18   2.18

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     1.643     0    0.610   0.911     5.284   79.286   63.413
LGA    L     6_B      L     6_B     0.521     0    0.073   1.247     2.529   95.238   85.476
LGA    E     7_B      E     7_B     0.521     0    0.074   0.947     4.159   95.238   76.931
LGA    T     8_B      T     8_B     0.553     0    0.036   1.220     2.649   92.857   82.313
LGA    K     9_B      K     9_B     0.547     0    0.019   0.095     0.918   90.476   90.476
LGA    K    10_B      K    10_B     0.500     0    0.037   0.841     2.681   92.857   86.931
LGA    A    11_B      A    11_B     0.723     0    0.030   0.045     0.876   90.476   90.476
LGA    Y    12_B      Y    12_B     0.844     0    0.018   0.080     1.575   88.214   83.730
LGA    A    13_B      A    13_B     0.860     0    0.011   0.020     0.952   90.476   90.476
LGA    A    14_B      A    14_B     0.890     0    0.045   0.055     1.199   85.952   86.857
LGA    R    15_B      R    15_B     1.268     0    0.025   0.834     2.627   79.286   80.087
LGA    T    16_B      T    16_B     1.553     0    0.041   0.045     1.822   79.286   77.755
LGA    R    17_B      R    17_B     0.931     0    0.031   1.025     3.247   83.690   81.082
LGA    R    18_B      R    18_B     1.603     0    0.033   0.616     1.863   75.000   74.416
LGA    S    19_B      S    19_B     2.007     0    0.035   0.627     3.062   70.833   66.349
LGA    N    20_B      N    20_B     1.582     0    0.050   0.498     1.708   77.143   79.286
LGA    Y    21_B      Y    21_B     1.101     0    0.055   0.131     1.333   81.429   85.952
LGA    A    22_B      A    22_B     1.573     0    0.055   0.052     1.648   75.000   74.571
LGA    A    23_B      A    23_B     1.671     0    0.036   0.042     1.709   75.000   74.571
LGA    S    24_B      S    24_B     1.373     0    0.064   0.125     1.533   79.286   80.000
LGA    L    25_B      L    25_B     1.336     0    0.020   0.056     1.383   81.429   81.429
LGA    R    26_B      R    26_B     1.436     0    0.017   1.004     3.778   81.429   74.242
LGA    L    27_B      L    27_B     1.332     0    0.041   0.205     2.172   81.429   78.274
LGA    E    28_B      E    28_B     1.131     0    0.051   0.658     1.613   81.429   80.529
LGA    G    29_B      G    29_B     1.558     0    0.037   0.037     1.558   75.000   75.000
LGA    F    30_B      F    30_B     1.500     0    0.066   0.108     1.878   79.286   78.312
LGA    K    31_B      K    31_B     1.716     0    0.028   0.640     6.514   77.143   55.238
LGA    V    32_B      V    32_B     0.719     0    0.041   1.237     3.460   85.952   78.435
LGA    T    33_B      T    33_B     1.005     0    0.065   1.086     3.551   85.952   78.571
LGA    F    34_B      F    34_B     1.641     0    0.018   0.853     3.393   75.000   70.346
LGA    A    35_B      A    35_B     1.559     0    0.023   0.024     1.713   75.000   76.286
LGA    D    36_B      D    36_B     1.140     0    0.017   0.181     1.599   79.286   84.940
LGA    G    37_B      G    37_B     1.820     0    0.019   0.019     2.480   68.810   68.810
LGA    E    38_B      E    38_B     2.653     0    0.012   0.739     3.806   57.262   53.333
LGA    R    39_B      R    39_B     2.722     0    0.111   1.259     5.171   59.048   52.944
LGA    K    40_B      K    40_B     2.502     0    0.061   1.217     5.783   57.143   55.979
LGA    M    41_B      M    41_B     2.470     0    0.039   0.809     4.770   64.762   57.738
LGA    P    42_B      P    42_B     2.306     0    0.043   0.048     2.897   60.952   62.585
LGA    T    43_B      T    43_B     3.199     0    0.011   0.080     3.482   51.786   51.020
LGA    R    44_B      R    44_B     4.298     0    0.605   0.846    10.143   40.238   21.688
LGA    E    45_B      E    45_B     4.926     0    0.470   1.459     9.651   31.548   21.376
LGA    E    46_B      E    46_B     7.277     0    0.588   1.453    12.471   16.548    7.513
LGA    V    47_B      V    47_B     4.254     0    0.407   1.367     6.848   34.286   29.728

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     2.182          2.120                  2.889           73.901   69.895

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     42    1.94    86.047    90.047     2.058

LGA_LOCAL      RMSD:   1.941  Number of atoms:   42  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.216  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   2.182  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.135936 * X  +   0.900002 * Y  +   0.414146 * Z  +  25.404715
  Y_new =  -0.557972 * X  +  -0.414973 * Y  +   0.718655 * Z  + -33.040970
  Z_new =   0.818651 * X  +  -0.133391 * Y  +   0.558586 * Z  +  18.498703 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.809766 -0.959058 -0.234411   [DEG: -103.6920  -54.9500  -13.4308 ]
ZXZ:  2.618797  0.978117  1.732317   [DEG:  150.0460   56.0420   99.2544 ]
 
# END of job
