
#######################################################
#                                                     #
#                        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        3.94     3.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_B - 36_B        1.86     4.69
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.83     4.77
  LCS_AVERAGE:     74.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21       5_B - 25_B        0.87     5.32
  LONGEST_CONTINUOUS_SEGMENT:    21       7_B - 27_B        0.99     5.75
  LCS_AVERAGE:     42.06

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    5   41      3    4    4    5    6    9    9   10   10   11   13   20   36   37   39   40   40   40   41   41 
LCS_GDT     S     3_B     S     3_B      4   30   41      3    4    4    5    6   20   24   29   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     Q     4_B     Q     4_B      4   33   41      3    3    4    5   19   25   31   32   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     R     5_B     R     5_B     21   33   41      5   13   20   25   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     L     6_B     L     6_B     21   33   41      5   17   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     F     7_B     F     7_B     21   33   41      5   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     V     8_B     V     8_B     21   33   41     11   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     L     9_B     L     9_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     D    10_B     D    10_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     N    11_B     N    11_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     E    12_B     E    12_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     R    13_B     R    13_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     Y    14_B     Y    14_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     D    15_B     D    15_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     S    16_B     S    16_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     F    17_B     F    17_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     I    18_B     I    18_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     T    19_B     T    19_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     Q    20_B     Q    20_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     L    21_B     L    21_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     E    22_B     E    22_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     A    23_B     A    23_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     P    24_B     P    24_B     21   33   41     15   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     V    25_B     V    25_B     21   33   41      3    5   21   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     Q    26_B     Q    26_B     21   33   41     12   13   14   15   22   28   32   33   33   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     N    27_B     N    27_B     21   33   41     12   18   21   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     A    28_B     A    28_B     15   33   41     12   13   21   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     E    29_B     E    29_B     15   33   41     12   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     G    30_B     G    30_B     15   33   41     12   13   19   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     R    31_B     R    31_B     15   33   41     12   18   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     E    32_B     E    32_B     15   33   41     12   19   22   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     R    33_B     R    33_B     15   33   41     12   13   14   24   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     L    34_B     L    34_B     15   33   41     12   13   14   18   28   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     M    35_B     M    35_B     15   33   41     12   13   21   26   29   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     A    36_B     A    36_B     15   33   41     12   13   14   20   28   31   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     V    37_B     V    37_B     15   33   41     12   13   14   15   17   26   32   33   34   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     K    38_B     K    38_B     15   18   41     10   13   14   15   16   17   26   31   33   35   36   36   37   38   39   40   40   40   41   41 
LCS_GDT     P    39_B     P    39_B     15   18   41      3   10   14   15   16   16   16   17   23   28   31   34   37   38   39   40   40   40   41   41 
LCS_GDT     E    40_B     E    40_B     15   18   41      3    5    6   15   16   16   16   17   18   19   20   26   31   34   37   40   40   40   41   41 
LCS_GDT     W    41_B     W    41_B     15   18   41      3   12   14   15   16   16   16   17   18   21   24   32   35   36   39   40   40   40   41   41 
LCS_GDT     K    42_B     K    42_B      3   18   41      3    3    3    4    4    4   12   16   17   18   22   27   35   38   39   40   40   40   41   41 
LCS_AVERAGE  LCS_A:  72.08  (  42.06   74.18  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     15     19     22     26     29     31     32     33     34     35     36     36     37     38     39     40     40     40     41     41 
GDT PERCENT_AT  36.59  46.34  53.66  63.41  70.73  75.61  78.05  80.49  82.93  85.37  87.80  87.80  90.24  92.68  95.12  97.56  97.56  97.56 100.00 100.00
GDT RMS_LOCAL    0.27   0.57   0.74   1.03   1.25   1.46   1.69   1.83   2.12   2.23   2.44   2.44   2.79   3.13   3.44   3.63   3.63   3.63   3.94   3.94
GDT RMS_ALL_AT   4.50   5.04   5.08   5.20   5.04   4.88   4.73   4.77   4.38   4.41   4.31   4.31   4.16   4.03   3.97   3.96   3.96   3.96   3.94   3.94

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_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    11.725     0    0.236   0.332    13.481    2.143    1.714
LGA    S     3_B      S     3_B     7.298     0    0.178   0.703     9.011   11.429   19.524
LGA    Q     4_B      Q     4_B     5.986     0    0.166   0.778    13.069   23.333   11.217
LGA    R     5_B      R     5_B     2.104     0    0.640   1.153    12.520   68.810   34.589
LGA    L     6_B      L     6_B     1.298     0    0.067   0.093     1.497   81.429   82.560
LGA    F     7_B      F     7_B     1.234     0    0.079   0.083     1.435   81.429   81.429
LGA    V     8_B      V     8_B     1.185     0    0.039   1.184     2.369   81.429   76.667
LGA    L     9_B      L     9_B     0.919     0    0.026   0.126     1.151   88.214   84.821
LGA    D    10_B      D    10_B     1.006     0    0.087   0.631     1.817   88.214   84.881
LGA    N    11_B      N    11_B     0.509     0    0.026   0.958     3.042   90.476   82.083
LGA    E    12_B      E    12_B     0.945     0    0.050   1.123     6.726   88.214   62.910
LGA    R    13_B      R    13_B     1.022     0    0.015   1.126     2.997   88.214   77.836
LGA    Y    14_B      Y    14_B     0.622     0    0.040   0.166     1.121   90.476   89.762
LGA    D    15_B      D    15_B     0.416     0    0.016   0.455     1.120  100.000   96.488
LGA    S    16_B      S    16_B     0.518     0    0.023   0.172     0.663   92.857   92.063
LGA    F    17_B      F    17_B     0.632     0    0.032   0.250     1.195   90.476   88.009
LGA    I    18_B      I    18_B     0.547     0    0.013   0.118     0.782   95.238   95.238
LGA    T    19_B      T    19_B     0.425     0    0.023   0.249     0.706   95.238   94.558
LGA    Q    20_B      Q    20_B     0.703     0    0.008   1.153     2.980   90.476   80.847
LGA    L    21_B      L    21_B     1.094     0    0.018   1.321     3.055   83.690   77.679
LGA    E    22_B      E    22_B     0.936     0    0.092   0.745     1.947   90.476   83.545
LGA    A    23_B      A    23_B     0.432     0    0.067   0.097     0.729   92.857   94.286
LGA    P    24_B      P    24_B     0.656     0    0.032   0.360     1.376   85.952   90.612
LGA    V    25_B      V    25_B     2.303     0    0.101   1.264     5.091   68.810   58.503
LGA    Q    26_B      Q    26_B     4.335     0    0.691   0.695     8.739   33.690   20.688
LGA    N    27_B      N    27_B     2.282     0    0.143   0.129     2.508   64.881   65.833
LGA    A    28_B      A    28_B     2.622     0    0.038   0.039     3.500   65.000   60.667
LGA    E    29_B      E    29_B     1.391     0    0.046   0.851     3.344   81.548   68.148
LGA    G    30_B      G    30_B     1.581     0    0.119   0.119     1.746   77.262   77.262
LGA    R    31_B      R    31_B     1.586     0    0.079   1.202    10.468   83.810   46.234
LGA    E    32_B      E    32_B     0.952     0    0.046   0.847     5.595   83.810   61.958
LGA    R    33_B      R    33_B     2.261     0    0.078   1.172     4.020   61.190   58.182
LGA    L    34_B      L    34_B     2.731     0    0.035   1.396     6.619   57.262   50.179
LGA    M    35_B      M    35_B     1.534     0    0.058   1.144     6.689   70.833   60.774
LGA    A    36_B      A    36_B     3.006     0    0.039   0.038     4.532   47.381   47.905
LGA    V    37_B      V    37_B     4.961     0    0.041   0.087     6.173   30.238   27.959
LGA    K    38_B      K    38_B     6.565     4    0.147   0.166     9.560    8.929    5.079
LGA    P    39_B      P    39_B     9.759     0    0.050   0.076    10.309    1.667    3.741
LGA    E    40_B      E    40_B    12.695     0    0.407   1.046    20.231    0.000    0.000
LGA    W    41_B      W    41_B    12.539     0    0.407   1.037    13.470    0.000    0.000
LGA    K    42_B      K    42_B    11.761     0    0.547   1.306    17.109    1.190    0.529

# 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):     3.943          3.873                  4.973           64.355   58.462

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     33    1.83    71.951    74.515     1.709

LGA_LOCAL      RMSD:   1.831  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.768  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   3.943  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.235662 * X  +  -0.445660 * Y  +  -0.863627 * Z  +   7.827917
  Y_new =   0.850285 * X  +  -0.335783 * Y  +   0.405296 * Z  + -25.614790
  Z_new =  -0.470616 * X  +  -0.829841 * Y  +   0.299807 * Z  +  47.943649 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.300427  0.489989 -1.224106   [DEG:   74.5090   28.0743  -70.1361 ]
ZXZ: -2.009580  1.266306 -2.625704   [DEG: -115.1405   72.5540 -150.4418 ]
 
# END of job
