
#######################################################
#                                                     #
#                        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:    38       5_B - 42_B        4.99     6.46
  LONGEST_CONTINUOUS_SEGMENT:    38       6_B - 43_B        4.98     6.37
  LONGEST_CONTINUOUS_SEGMENT:    38       7_B - 44_B        4.96     6.33
  LONGEST_CONTINUOUS_SEGMENT:    38       8_B - 45_B        4.98     6.37
  LCS_AVERAGE:     87.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      16_B - 35_B        1.84     9.32
  LCS_AVERAGE:     36.40

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      17_B - 32_B        0.95    10.17
  LCS_AVERAGE:     26.39

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     14   17   38     10   13   13   14   15   16   17   19   20   21   23   27   30   33   35   38   40   42   42   42 
LCS_GDT     L     6_B     L     6_B     14   17   38     11   13   13   14   15   16   17   19   20   22   23   28   30   34   35   38   40   42   42   42 
LCS_GDT     E     7_B     E     7_B     14   17   38     11   13   13   14   15   16   17   19   20   22   24   31   33   34   35   38   40   42   42   42 
LCS_GDT     T     8_B     T     8_B     14   17   38     11   13   13   14   15   16   17   19   20   26   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     K     9_B     K     9_B     14   17   38     11   13   13   14   15   16   17   19   23   27   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     K    10_B     K    10_B     14   17   38     11   13   13   14   15   16   17   20   25   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     A    11_B     A    11_B     14   17   38     11   13   13   14   15   16   17   20   25   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     Y    12_B     Y    12_B     14   17   38     11   13   13   14   15   16   21   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     A    13_B     A    13_B     14   17   38     11   13   13   14   15   18   23   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     A    14_B     A    14_B     14   17   38     11   13   13   14   15   18   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     R    15_B     R    15_B     14   19   38     11   13   13   14   15   16   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     T    16_B     T    16_B     15   20   38     11   13   14   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     R    17_B     R    17_B     16   20   38      4   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     R    18_B     R    18_B     16   20   38      5   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     S    19_B     S    19_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     N    20_B     N    20_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     Y    21_B     Y    21_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     A    22_B     A    22_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     A    23_B     A    23_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     S    24_B     S    24_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     L    25_B     L    25_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     R    26_B     R    26_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     L    27_B     L    27_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     E    28_B     E    28_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     G    29_B     G    29_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     F    30_B     F    30_B     16   20   38      8   13   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     K    31_B     K    31_B     16   20   38      3    4   12   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     V    32_B     V    32_B     16   20   38      3   10   15   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     T    33_B     T    33_B      5   20   38      3    5    6   10   16   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     F    34_B     F    34_B      5   20   38      3    5    5    7   10   16   23   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     A    35_B     A    35_B      5   20   38      3    7   11   17   18   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     D    36_B     D    36_B      5   17   38      3    3    5    7    9   13   20   22   22   27   27   29   32   34   36   38   40   42   42   42 
LCS_GDT     G    37_B     G    37_B      3    5   38      3    3    3    6   15   18   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     E    38_B     E    38_B      3    5   38      3    4    7   10   15   19   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     R    39_B     R    39_B      3    5   38      3    4    6   10   15   18   24   26   27   29   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     K    40_B     K    40_B      3    7   38      3    3    4    9   11   15   16   19   20   26   31   32   33   34   36   38   40   42   42   42 
LCS_GDT     M    41_B     M    41_B      5    7   38      4    5    5    5    6    7   16   19   20   22   25   29   32   34   36   38   40   42   42   42 
LCS_GDT     P    42_B     P    42_B      5    7   38      4    5    5    5    7    7    9   10   19   21   23   27   30   33   35   38   40   42   42   42 
LCS_GDT     T    43_B     T    43_B      5    7   38      4    5    5    5    7    7    9   10   12   21   24   29   32   34   36   38   40   42   42   42 
LCS_GDT     R    44_B     R    44_B      5    7   38      4    5    5    5    7    7    9   10   17   25   26   29   32   33   36   38   40   42   42   42 
LCS_GDT     E    45_B     E    45_B      5    7   38      4    5    5    5    7    7    9   10   13   20   24   29   32   33   36   38   40   42   42   42 
LCS_GDT     E    46_B     E    46_B      3    7   37      3    3    3    3    4    6    7    9   12   13   15   26   30   33   34   36   40   42   42   42 
LCS_GDT     V    47_B     V    47_B      3    3   17      3    3    3    3    3    3    4    5    6   10   12   13   13   14   15   17   17   22   28   34 
LCS_AVERAGE  LCS_A:  49.99  (  26.39   36.40   87.18 )

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     11     13     15     17     18     19     24     26     27     29     31     32     33     34     36     38     40     42     42     42 
GDT PERCENT_AT  25.58  30.23  34.88  39.53  41.86  44.19  55.81  60.47  62.79  67.44  72.09  74.42  76.74  79.07  83.72  88.37  93.02  97.67  97.67  97.67
GDT RMS_LOCAL    0.25   0.40   0.85   1.11   1.22   1.46   2.44   2.64   2.78   3.32   3.68   3.87   4.11   4.33   4.57   4.98   5.26   5.61   5.61   5.61
GDT RMS_ALL_AT  12.98  12.97  10.16   9.97   9.62   9.55   8.12   7.80   7.53   7.08   6.84   6.71   6.67   6.70   6.50   6.37   6.25   6.11   6.11   6.11

# Checking swapping
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  D    36_B      D    36_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B    18.400     0    0.646   0.677    22.264    0.000    0.000
LGA    L     6_B      L     6_B    17.291     0    0.046   1.410    19.807    0.000    0.000
LGA    E     7_B      E     7_B    15.534     0    0.046   1.203    22.281    0.000    0.000
LGA    T     8_B      T     8_B    12.861     0    0.076   0.146    14.754    0.000    0.000
LGA    K     9_B      K     9_B    11.405     0    0.030   1.164    14.189    0.714    0.317
LGA    K    10_B      K    10_B     9.927     0    0.037   0.920    17.645    3.333    1.481
LGA    A    11_B      A    11_B     8.766     0    0.031   0.037     9.892    7.857    6.381
LGA    Y    12_B      Y    12_B     5.707     0    0.031   1.107    11.618   28.214   12.817
LGA    A    13_B      A    13_B     4.351     0    0.024   0.038     5.423   46.548   42.476
LGA    A    14_B      A    14_B     3.744     0    0.075   0.072     5.549   46.667   41.619
LGA    R    15_B      R    15_B     3.601     0    0.132   1.692    11.281   50.357   28.095
LGA    T    16_B      T    16_B     1.289     0    0.230   1.076     3.052   77.381   71.020
LGA    R    17_B      R    17_B     2.361     0    0.079   1.207     9.731   61.190   36.537
LGA    R    18_B      R    18_B     3.060     0    0.058   0.936     5.814   50.119   41.861
LGA    S    19_B      S    19_B     3.423     0    0.634   0.967     5.178   42.381   46.111
LGA    N    20_B      N    20_B     2.907     0    0.102   0.431     2.937   57.143   62.024
LGA    Y    21_B      Y    21_B     2.885     0    0.051   1.517    10.606   59.048   32.183
LGA    A    22_B      A    22_B     2.468     0    0.037   0.056     2.682   66.905   64.952
LGA    A    23_B      A    23_B     1.077     0    0.045   0.053     1.735   86.190   85.238
LGA    S    24_B      S    24_B     1.371     0    0.041   0.674     2.452   83.690   78.730
LGA    L    25_B      L    25_B     1.097     0    0.060   0.233     3.017   85.952   73.571
LGA    R    26_B      R    26_B     0.748     0    0.052   0.981     5.349   88.214   64.329
LGA    L    27_B      L    27_B     1.262     0    0.051   1.012     6.156   77.381   60.774
LGA    E    28_B      E    28_B     1.413     0    0.135   1.170     6.001   79.286   64.656
LGA    G    29_B      G    29_B     1.540     0    0.081   0.081     1.944   75.000   75.000
LGA    F    30_B      F    30_B     1.383     0    0.071   0.153     2.685   75.119   72.338
LGA    K    31_B      K    31_B     3.050     0    0.248   0.703     8.878   59.167   35.238
LGA    V    32_B      V    32_B     2.600     0    0.097   1.331     5.713   59.048   53.401
LGA    T    33_B      T    33_B     2.730     0    0.062   1.113     5.078   60.952   52.857
LGA    F    34_B      F    34_B     3.784     0    0.645   1.446    11.555   50.119   23.377
LGA    A    35_B      A    35_B     3.250     0    0.630   0.613     4.752   45.833   46.667
LGA    D    36_B      D    36_B     6.087     0    0.086   1.076    11.961   30.952   16.071
LGA    G    37_B      G    37_B     2.988     0    0.504   0.504     2.988   59.048   59.048
LGA    E    38_B      E    38_B     2.620     0    0.211   1.200     8.708   54.048   33.757
LGA    R    39_B      R    39_B     2.695     0    0.557   1.472     8.578   46.310   38.571
LGA    K    40_B      K    40_B     7.848     0    0.053   0.987    13.823   12.262    5.450
LGA    M    41_B      M    41_B     8.617     0    0.206   0.987    10.308    1.548    7.083
LGA    P    42_B      P    42_B    10.872     0    0.087   0.373    12.038    1.310    0.748
LGA    T    43_B      T    43_B     9.031     0    0.096   0.100    10.807    1.071    0.680
LGA    R    44_B      R    44_B     8.415     0    0.581   1.050    11.538    3.095    5.541
LGA    E    45_B      E    45_B    10.747     0    0.469   1.247    13.868    0.357    1.111
LGA    E    46_B      E    46_B    12.222     0    0.581   1.204    16.737    0.000    0.000
LGA    V    47_B      V    47_B    18.567     0    0.437   1.364    20.241    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):     6.085          6.082                  6.931           40.321   33.538

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     26    2.64    54.651    50.470     0.949

LGA_LOCAL      RMSD:   2.640  Number of atoms:   26  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.801  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   6.085  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.595811 * X  +  -0.479849 * Y  +   0.644014 * Z  + -10.245427
  Y_new =   0.415351 * X  +  -0.870424 * Y  +  -0.264283 * Z  + -49.037212
  Z_new =   0.687382 * X  +   0.110029 * Y  +   0.717914 * Z  +  19.276909 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.532803 -0.757878  0.152079   [DEG:  145.1189  -43.4232    8.7135 ]
ZXZ:  1.181383  0.769996  1.412073   [DEG:   67.6883   44.1175   80.9058 ]
 
# END of job
