
#######################################################
#                                                     #
#                        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:    42       5_B - 46_B        4.58     5.05
  LONGEST_CONTINUOUS_SEGMENT:    42       6_B - 47_B        5.00     5.06
  LCS_AVERAGE:     97.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        1.82     5.26
  LCS_AVERAGE:     49.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       6_B - 29_B        0.96     5.63
  LCS_AVERAGE:     39.05

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     23   28   42      6   10   18   23   24   26   27   30   31   32   34   34   36   36   38   39   39   40   42   42 
LCS_GDT     L     6_B     L     6_B     24   28   42      6   17   22   24   25   26   28   30   31   32   34   34   36   36   38   39   39   41   42   42 
LCS_GDT     E     7_B     E     7_B     24   28   42      6   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     T     8_B     T     8_B     24   28   42      6   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     K     9_B     K     9_B     24   28   42      7   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     K    10_B     K    10_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     A    11_B     A    11_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     Y    12_B     Y    12_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     A    13_B     A    13_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     A    14_B     A    14_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     R    15_B     R    15_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     T    16_B     T    16_B     24   28   42     12   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     R    17_B     R    17_B     24   28   42     12   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     R    18_B     R    18_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     S    19_B     S    19_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     N    20_B     N    20_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     Y    21_B     Y    21_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     A    22_B     A    22_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     A    23_B     A    23_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     S    24_B     S    24_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     L    25_B     L    25_B     24   28   42     10   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     R    26_B     R    26_B     24   28   42     10   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     L    27_B     L    27_B     24   28   42     14   19   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     E    28_B     E    28_B     24   28   42      8   17   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     G    29_B     G    29_B     24   28   42      8   17   22   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     F    30_B     F    30_B     22   28   42      4   13   18   24   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     K    31_B     K    31_B     19   28   42      3   11   18   21   25   27   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     V    32_B     V    32_B      9   28   42      5    5   14   19   24   27   28   28   29   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     T    33_B     T    33_B      6   24   42      5    5    6    7   12   17   20   23   26   29   31   32   33   36   38   39   40   41   42   42 
LCS_GDT     F    34_B     F    34_B      6   16   42      5    5    6    9   12   17   20   23   26   27   31   32   33   34   38   39   40   41   42   42 
LCS_GDT     A    35_B     A    35_B      6   16   42      5    5    8   14   20   23   27   28   29   30   31   32   34   36   38   39   40   41   42   42 
LCS_GDT     D    36_B     D    36_B      6   16   42      5    8   17   19   24   27   28   28   29   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     G    37_B     G    37_B      5    8   42      3    4    5    6    6    8   11   21   25   30   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     E    38_B     E    38_B      5    7   42      3    4    5    6    6    8   11   18   22   24   28   34   36   36   38   39   40   41   42   42 
LCS_GDT     R    39_B     R    39_B      5    7   42      3    4    5    6    6    8   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     K    40_B     K    40_B      3    6   42      3    3    4    5    6    7   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     M    41_B     M    41_B      5    6   42      4    5    5    5    9   26   28   30   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     P    42_B     P    42_B      5    6   42      4    5    5    5    8   16   23   26   31   32   34   34   36   36   38   39   40   41   42   42 
LCS_GDT     T    43_B     T    43_B      5    6   42      4    5    5    5    6   10   15   18   24   29   30   33   36   36   38   39   40   41   42   42 
LCS_GDT     R    44_B     R    44_B      5    6   42      4    5    5    5    5    6    7   13   17   22   24   27   29   31   37   37   40   41   42   42 
LCS_GDT     E    45_B     E    45_B      5    6   42      3    5    5    5    5    6    7   10   14   18   20   26   29   31   37   37   40   41   42   42 
LCS_GDT     E    46_B     E    46_B      3    6   42      3    3    3    3    4    6    6    8    8    9   20   23   27   33   37   37   40   41   42   42 
LCS_GDT     V    47_B     V    47_B      3    3   42      0    3    3    3    3    3    4    6    7    7    7    8    9    9   13   20   26   28   29   37 
LCS_AVERAGE  LCS_A:  62.21  (  39.05   49.92   97.67 )

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     14     19     22     24     25     27     28     30     31     32     34     34     36     36     38     39     40     41     42     42 
GDT PERCENT_AT  32.56  44.19  51.16  55.81  58.14  62.79  65.12  69.77  72.09  74.42  79.07  79.07  83.72  83.72  88.37  90.70  93.02  95.35  97.67  97.67
GDT RMS_LOCAL    0.34   0.55   0.75   0.96   1.16   1.71   1.63   1.86   2.02   2.37   2.66   2.66   3.03   3.03   3.61   3.85   4.49   4.53   4.58   4.58
GDT RMS_ALL_AT   5.64   5.65   5.79   5.63   5.47   5.20   5.59   5.55   5.50   5.29   5.25   5.25   5.21   5.21   5.14   5.16   5.09   5.06   5.05   5.05

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_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:  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     3.139     0    0.645   0.941     5.275   53.452   58.730
LGA    L     6_B      L     6_B     1.992     0    0.040   1.288     4.161   77.381   68.631
LGA    E     7_B      E     7_B     1.018     0    0.088   1.047     5.695   83.690   65.238
LGA    T     8_B      T     8_B     1.094     0    0.056   1.105     4.245   88.333   76.599
LGA    K     9_B      K     9_B     0.947     0    0.059   1.413     9.778   88.214   55.185
LGA    K    10_B      K    10_B     0.588     0    0.042   1.115     3.023   90.476   76.614
LGA    A    11_B      A    11_B     0.626     0    0.041   0.044     0.672   90.476   90.476
LGA    Y    12_B      Y    12_B     0.789     0    0.043   0.075     1.849   88.214   83.056
LGA    A    13_B      A    13_B     1.042     0    0.027   0.093     1.308   83.690   83.238
LGA    A    14_B      A    14_B     0.627     0    0.072   0.068     0.791   90.476   90.476
LGA    R    15_B      R    15_B     1.334     0    0.101   0.927     7.066   81.429   55.498
LGA    T    16_B      T    16_B     1.525     0    0.088   1.059     3.393   75.000   72.041
LGA    R    17_B      R    17_B     1.396     0    0.049   0.951     3.763   81.429   74.892
LGA    R    18_B      R    18_B     0.916     0    0.038   0.975     5.057   88.214   62.338
LGA    S    19_B      S    19_B     1.180     0    0.043   0.703     3.125   81.429   76.190
LGA    N    20_B      N    20_B     1.235     0    0.048   0.412     2.823   81.429   76.250
LGA    Y    21_B      Y    21_B     1.077     0    0.042   0.235     1.939   85.952   78.651
LGA    A    22_B      A    22_B     0.807     0    0.039   0.045     0.913   90.476   90.476
LGA    A    23_B      A    23_B     1.173     0    0.030   0.036     1.364   83.690   83.238
LGA    S    24_B      S    24_B     1.133     0    0.036   0.590     2.799   83.690   78.889
LGA    L    25_B      L    25_B     0.580     0    0.096   0.894     3.171   92.857   85.476
LGA    R    26_B      R    26_B     0.796     0    0.070   1.223     7.485   90.476   61.905
LGA    L    27_B      L    27_B     1.649     0    0.068   1.458     4.155   77.143   69.524
LGA    E    28_B      E    28_B     1.833     0    0.103   0.693     2.825   72.976   67.566
LGA    G    29_B      G    29_B     1.174     0    0.086   0.086     2.479   75.119   75.119
LGA    F    30_B      F    30_B     2.791     0    0.106   0.685     5.601   60.952   46.926
LGA    K    31_B      K    31_B     4.201     0    0.352   1.107     6.187   30.952   37.302
LGA    V    32_B      V    32_B     6.239     0    0.123   0.318     7.941   14.405   18.707
LGA    T    33_B      T    33_B    11.110     0    0.044   0.992    15.264    1.071    0.612
LGA    F    34_B      F    34_B    11.844     0    0.039   0.119    14.183    0.119    0.043
LGA    A    35_B      A    35_B    11.419     0    0.072   0.071    13.171    1.548    1.238
LGA    D    36_B      D    36_B     7.237     0    0.534   0.494    11.164   17.500    9.702
LGA    G    37_B      G    37_B     6.901     0    0.407   0.407     6.901   13.333   13.333
LGA    E    38_B      E    38_B     7.184     0    0.718   0.536    11.408   13.690    6.667
LGA    R    39_B      R    39_B     3.569     0    0.115   1.653     8.138   48.452   30.260
LGA    K    40_B      K    40_B     3.838     0    0.069   0.662    11.875   40.476   21.640
LGA    M    41_B      M    41_B     2.889     0    0.651   1.015     8.452   54.286   37.262
LGA    P    42_B      P    42_B     4.884     0    0.033   0.495     5.795   29.405   34.830
LGA    T    43_B      T    43_B     7.231     0    0.051   0.047     8.821    8.690    7.823
LGA    R    44_B      R    44_B    10.392     0    0.577   1.415    12.778    0.357    0.130
LGA    E    45_B      E    45_B    12.254     0    0.454   1.205    14.535    0.000    0.000
LGA    E    46_B      E    46_B     9.234     0    0.598   1.112    11.735    0.476    1.958
LGA    V    47_B      V    47_B    14.768     0    0.475   1.303    16.940    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):     5.041          4.976                  5.800           56.080   49.412

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     30    1.86    65.116    62.194     1.531

LGA_LOCAL      RMSD:   1.860  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.553  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   5.041  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.983852 * X  +   0.171030 * Y  +   0.052758 * Z  +  15.870157
  Y_new =  -0.145428 * X  +  -0.935715 * Y  +   0.321386 * Z  + -67.719627
  Z_new =   0.104333 * X  +   0.308524 * Y  +   0.945478 * Z  +  15.282452 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.994841 -0.104523  0.315421   [DEG: -171.5917   -5.9887   18.0723 ]
ZXZ:  2.978887  0.331739  0.326095   [DEG:  170.6777   19.0072   18.6839 ]
 
# END of job
