
#######################################################
#                                                     #
#                        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   56 (  447),  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        3.89     3.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       5_B - 40_B        1.83     4.82
  LONGEST_CONTINUOUS_SEGMENT:    36       6_B - 41_B        1.98     4.63
  LCS_AVERAGE:     78.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       8_B - 31_B        0.99     5.40
  LCS_AVERAGE:     45.65

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     22   36   43     13   17   21   27   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     22   36   43     13   17   21   27   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     22   36   43     13   17   24   27   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     24   36   43     13   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     24   36   43      7   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     24   36   43      9   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     24   36   43      9   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     24   36   43      9   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     24   36   43     10   17   24   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     23   36   43      9   16   23   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     23   36   43      8   15   23   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     23   36   43      5   13   23   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     21   36   43      5   11   21   26   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     18   36   43      5    8   19   25   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     10   36   43      5   14   21   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     10   36   43      5   15   22   28   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     10   36   43      6   15   21   26   32   34   35   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     10   36   43      6   10   21   25   28   32   34   36   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     10   36   43      6    8   12   23   26   30   34   35   37   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     10   33   43      6    8   12   21   25   27   30   35   36   37   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     10   30   43      6    8   12   17   23   26   28   32   36   36   39   40   40   40   40   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     10   29   43      6    8   12   17   21   26   28   32   34   36   38   40   40   40   40   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      8   14   43      3    7    9   16   19   21   26   28   30   32   34   35   39   40   40   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   13   43      3    3    5    5    5    8   10   17   24   27   30   35   39   40   40   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    6   29   32   32   35   39   40   40   41   43   43   43   43 
LCS_AVERAGE  LCS_A:  74.76  (  45.65   78.64  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     13     17     24     28     32     34     35     36     37     37     39     40     40     40     40     42     43     43     43     43 
GDT PERCENT_AT  30.23  39.53  55.81  65.12  74.42  79.07  81.40  83.72  86.05  86.05  90.70  93.02  93.02  93.02  93.02  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.19   0.50   0.99   1.20   1.41   1.59   1.68   1.83   2.01   2.01   2.58   2.84   2.84   2.84   2.84   3.61   3.89   3.89   3.89   3.89
GDT RMS_ALL_AT   6.91   6.40   5.40   4.90   5.08   4.98   4.93   4.82   4.70   4.70   4.33   4.17   4.17   4.17   4.17   3.91   3.89   3.89   3.89   3.89

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.568     0    0.027   0.172     3.500   60.952   57.302
LGA    L     6_B      L     6_B     2.892     0    0.033   0.874     3.456   59.048   57.202
LGA    E     7_B      E     7_B     2.487     0    0.034   1.104     7.226   66.905   49.153
LGA    T     8_B      T     8_B     0.955     0    0.070   1.232     3.025   86.071   78.503
LGA    K     9_B      K     9_B     1.121     0    0.014   0.182     2.424   83.690   74.974
LGA    K    10_B      K    10_B     1.520     0    0.010   0.943     5.748   79.286   61.534
LGA    A    11_B      A    11_B     1.504     0    0.019   0.019     1.770   79.286   78.000
LGA    Y    12_B      Y    12_B     0.775     0    0.018   1.238     8.075   88.214   58.730
LGA    A    13_B      A    13_B     0.339     0    0.016   0.017     0.865   97.619   96.190
LGA    A    14_B      A    14_B     1.481     0    0.055   0.063     2.124   77.381   74.857
LGA    R    15_B      R    15_B     2.183     0    0.016   1.175     4.526   64.881   63.074
LGA    T    16_B      T    16_B     2.094     0    0.073   0.094     2.479   70.833   69.388
LGA    R    17_B      R    17_B     0.990     0    0.041   0.744     3.744   85.952   67.662
LGA    R    18_B      R    18_B     1.411     0    0.027   1.247     6.875   79.286   57.532
LGA    S    19_B      S    19_B     2.190     0    0.043   0.700     2.797   70.833   68.889
LGA    N    20_B      N    20_B     1.835     0    0.030   0.352     2.284   77.143   73.988
LGA    Y    21_B      Y    21_B     0.480     0    0.093   0.228     5.317   97.619   68.175
LGA    A    22_B      A    22_B     0.817     0    0.010   0.017     1.235   90.476   88.667
LGA    A    23_B      A    23_B     1.194     0    0.020   0.021     1.580   81.429   79.714
LGA    S    24_B      S    24_B     1.282     0    0.067   0.731     1.482   81.429   82.937
LGA    L    25_B      L    25_B     0.836     0    0.013   0.041     1.035   88.214   88.214
LGA    R    26_B      R    26_B     0.595     0    0.051   1.239     5.429   90.476   70.823
LGA    L    27_B      L    27_B     1.057     0    0.034   0.219     1.475   83.690   82.560
LGA    E    28_B      E    28_B     1.392     0    0.033   0.642     2.575   79.286   74.974
LGA    G    29_B      G    29_B     1.378     0    0.159   0.159     1.378   81.429   81.429
LGA    F    30_B      F    30_B     1.234     0    0.637   0.572     3.414   71.429   77.013
LGA    K    31_B      K    31_B     1.176     0    0.170   0.626     4.086   83.690   69.577
LGA    V    32_B      V    32_B     0.381     0    0.645   0.532     4.122   77.500   80.748
LGA    T    33_B      T    33_B     1.290     0    0.069   1.045     4.350   88.214   75.374
LGA    F    34_B      F    34_B     1.376     0    0.165   1.369     6.977   81.548   54.848
LGA    A    35_B      A    35_B     2.396     0    0.030   0.031     3.525   64.762   60.476
LGA    D    36_B      D    36_B     2.986     0    0.076   0.252     4.641   55.357   47.143
LGA    G    37_B      G    37_B     2.097     0    0.035   0.035     2.531   64.881   64.881
LGA    E    38_B      E    38_B     1.587     0    0.037   0.851     4.140   68.810   64.974
LGA    R    39_B      R    39_B     3.202     0    0.115   1.297     5.290   48.452   39.307
LGA    K    40_B      K    40_B     4.577     0    0.055   0.867    12.240   33.095   18.942
LGA    M    41_B      M    41_B     5.606     0    0.028   1.269     6.384   20.476   30.952
LGA    P    42_B      P    42_B     7.492     0    0.022   0.032     7.968    9.405    9.320
LGA    T    43_B      T    43_B     9.062     0    0.076   1.113    11.478    1.310    0.884
LGA    R    44_B      R    44_B     9.838     0    0.600   1.426    10.455    0.952   11.385
LGA    E    45_B      E    45_B    13.545     0    0.438   1.116    18.464    0.000    0.000
LGA    E    46_B      E    46_B    14.638     0    0.598   1.429    16.727    0.000    0.000
LGA    V    47_B      V    47_B    14.654     0    0.429   1.368    16.300    0.000    0.000

# 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):     3.885          3.807                  4.526           64.449   58.379

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     36    1.83    71.512    76.769     1.866

LGA_LOCAL      RMSD:   1.829  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.821  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.885  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.035099 * X  +  -0.937775 * Y  +  -0.345466 * Z  +  18.865580
  Y_new =  -0.860450 * X  +   0.204182 * Y  +  -0.466836 * Z  + -55.820328
  Z_new =   0.508325 * X  +   0.280871 * Y  +  -0.814075 * Z  +  10.091583 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.611565 -0.533238  2.809362   [DEG:  -92.3359  -30.5523  160.9646 ]
ZXZ: -0.637081  2.521930  1.066003   [DEG:  -36.5021  144.4960   61.0775 ]
 
# END of job
