
#######################################################
#                                                     #
#                        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   47 (  365),  selected   47 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   47 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      28_A - 57_A        4.97    19.65
  LONGEST_CONTINUOUS_SEGMENT:    30      29_A - 58_A        4.99    19.57
  LCS_AVERAGE:     43.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      41_A - 52_A        1.94    20.55
  LONGEST_CONTINUOUS_SEGMENT:    12      42_A - 53_A        1.48    20.34
  LCS_AVERAGE:     15.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      12_A - 21_A        0.90    32.50
  LCS_AVERAGE:     11.70

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   47
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    12_A     A    12_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   13   15   15   16   16   17   18   18   20 
LCS_GDT     V    13_A     V    13_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   13   15   15   16   16   17   18   19   20 
LCS_GDT     K    14_A     K    14_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   14   15   16   17   18   19   19   22   22 
LCS_GDT     A    15_A     A    15_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   14   15   16   17   18   19   19   22   23 
LCS_GDT     R    16_A     R    16_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   14   15   16   17   18   19   19   22   23 
LCS_GDT     V    17_A     V    17_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   14   15   16   17   18   19   20   25   26 
LCS_GDT     E    18_A     E    18_A     10   11   16      7    9    9   10   10   11   11   12   12   13   13   14   17   19   21   24   25   25   28   30 
LCS_GDT     K    19_A     K    19_A     10   11   16      4    9    9   10   10   11   11   12   12   13   14   16   17   19   21   24   25   26   29   30 
LCS_GDT     L    20_A     L    20_A     10   11   16      4    9    9   10   10   11   11   12   12   14   14   16   17   19   21   24   25   26   29   30 
LCS_GDT     A    21_A     A    21_A     10   11   20      3    4    4   10   10   11   11   12   12   14   14   17   19   20   21   24   25   26   29   30 
LCS_GDT     P    22_A     P    22_A      4   11   20      3    4    4    5    8   11   11   12   12   14   14   17   19   20   21   24   25   26   29   30 
LCS_GDT     E    23_A     E    23_A      4    6   20      3    4    4    5    8    8   10   12   12   13   14   17   19   20   21   22   23   25   28   30 
LCS_GDT     A    24_A     A    24_A      4    6   20      3    4    5    5    5    7    8   10   12   13   14   17   19   20   21   22   24   26   29   30 
LCS_GDT     V    25_A     V    25_A      4    6   20      3    4    5    5    5    7    8   10   11   12   14   17   19   20   21   22   24   26   29   30 
LCS_GDT     P    26_A     P    26_A      4    6   20      3    4    5    5    5    7    8   10   11   12   14   17   19   20   21   22   25   27   31   32 
LCS_GDT     Q    27_A     Q    27_A      4    6   20      3    4    5    5    5    7    8   10   11   12   14   17   20   23   24   28   30   32   32   32 
LCS_GDT     K    28_A     K    28_A      4    6   30      3    4    5    5    5    7    8   10   15   20   22   24   25   27   27   28   30   32   32   32 
LCS_GDT     L    29_A     L    29_A      3    4   30      3    3    4    4    4    7    8   14   17   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     K    30_A     K    30_A      3    4   30      3    3    4    5    7    8   10   16   17   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     R    31_A     R    31_A      3    4   30      3    3    4    4    9   11   14   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     A    32_A     A    32_A      3    4   30      3    3    4    6    9   11   15   18   18   21   21   24   25   27   27   29   30   32   32   32 
LCS_GDT     L    33_A     L    33_A      3    9   30      3    3    4    6    7    8   11   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     K    34_A     K    34_A      8    9   30      6    8    8    8   11   12   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     I    35_A     I    35_A      8    9   30      7    8    8    8    8    9   10   12   14   17   19   22   23   25   27   29   30   32   32   32 
LCS_GDT     A    36_A     A    36_A      8    9   30      7    8    8    8    8    8   10   11   14   16   18   22   23   25   27   29   30   32   32   32 
LCS_GDT     E    37_A     E    37_A      8    9   30      7    8    8    8    9   11   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     R    38_A     R    38_A      8    9   30      7    8    8    8    9   12   13   14   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     E    39_A     E    39_A      8    9   30      7    8    8    8    8    8   10   10   11   12   18   24   25   27   27   29   30   32   32   32 
LCS_GDT     Q    40_A     Q    40_A      8    9   30      7    8    8    8    8    8   10   10   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     G    41_A     G    41_A      8   12   30      7    8    8    8    9   12   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     E    42_A     E    42_A      3   12   30      3    3   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     G    43_A     G    43_A      3   12   30      3    3    5   11   12   13   13   15   17   18   20   23   25   27   27   29   30   32   32   32 
LCS_GDT     E    44_A     E    44_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     F    45_A     F    45_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     D    46_A     D    46_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     E    47_A     E    47_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     C    48_A     C    48_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     L    49_A     L    49_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     E    50_A     E    50_A      9   12   30      7    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     A    51_A     A    51_A      9   12   30      5    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     L    52_A     L    52_A      9   12   30      4    6   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     D    53_A     D    53_A      6   12   30      6    6    6   10   12   13   15   18   18   20   21   23   25   27   27   29   30   32   32   32 
LCS_GDT     D    54_A     D    54_A      6   11   30      6    6    6    6    6   11   13   14   15   17   19   21   25   27   27   29   30   32   32   32 
LCS_GDT     A    55_A     A    55_A      6    6   30      6    6    6    6    6    7   12   14   15   16   18   21   22   25   27   29   30   32   32   32 
LCS_GDT     K    56_A     K    56_A      6    6   30      6    8   10   11   12   13   15   18   18   21   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     R    57_A     R    57_A      6    6   30      6    6    6    6    6   10   13   14   18   20   22   24   25   27   27   29   30   32   32   32 
LCS_GDT     A    58_A     A    58_A      6    6   30      6    6    6    6    6    7    9   12   12   14   15   21   22   23   27   28   29   32   32   32 
LCS_AVERAGE  LCS_A:  23.40  (  11.70   15.46   43.05 )

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      7      9     10     11     12     13     15     18     18     21     22     24     25     27     27     29     30     32     32     32 
GDT PERCENT_AT  11.67  15.00  16.67  18.33  20.00  21.67  25.00  30.00  30.00  35.00  36.67  40.00  41.67  45.00  45.00  48.33  50.00  53.33  53.33  53.33
GDT RMS_LOCAL    0.22   0.53   0.78   0.99   1.32   1.56   2.23   2.69   2.69   3.56   3.90   4.18   4.03   4.47   4.47   4.78   4.97   5.57   5.57   5.57
GDT RMS_ALL_AT  32.76  32.48  20.07  19.91  19.98  20.16  20.45  20.79  20.79  19.95  19.47  19.55  20.00  19.76  19.76  19.79  19.65  19.27  19.27  19.27

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  F    45_A      F    45_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    54_A      D    54_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    12_A      A    12_A    39.704     0    0.454   0.467    40.179    0.000    0.000
LGA    V    13_A      V    13_A    36.545     0    0.000   1.000    37.655    0.000    0.000
LGA    K    14_A      K    14_A    38.673     0    0.048   1.180    40.116    0.000    0.000
LGA    A    15_A      A    15_A    40.383     0    0.051   0.046    41.433    0.000    0.000
LGA    R    16_A      R    16_A    36.831     0    0.037   1.121    37.850    0.000    0.000
LGA    V    17_A      V    17_A    35.366     0    0.083   0.150    36.368    0.000    0.000
LGA    E    18_A      E    18_A    38.639     0    0.085   1.117    45.473    0.000    0.000
LGA    K    19_A      K    19_A    40.185     0    0.129   0.965    47.101    0.000    0.000
LGA    L    20_A      L    20_A    37.384     0    0.614   0.547    38.138    0.000    0.000
LGA    A    21_A      A    21_A    37.473     0    0.039   0.050    37.877    0.000    0.000
LGA    P    22_A      P    22_A    35.774     0    0.632   0.753    37.051    0.000    0.000
LGA    E    23_A      E    23_A    35.464     0    0.667   1.075    40.461    0.000    0.000
LGA    A    24_A      A    24_A    29.111     0    0.680   0.627    31.611    0.000    0.000
LGA    V    25_A      V    25_A    24.573     0    0.196   0.195    26.261    0.000    0.000
LGA    P    26_A      P    26_A    21.241     0    0.064   0.156    23.025    0.000    0.000
LGA    Q    27_A      Q    27_A    17.005     0    0.623   1.532    20.209    0.000    0.000
LGA    K    28_A      K    28_A    10.995     0    0.013   0.827    13.187    1.548    0.688
LGA    L    29_A      L    29_A     8.245     0    0.623   1.469    10.192    5.119    2.976
LGA    K    30_A      K    30_A     7.013     0    0.614   0.533    10.645   13.690    8.042
LGA    R    31_A      R    31_A     3.983     0    0.378   1.333    13.804   49.762   22.078
LGA    A    32_A      A    32_A     3.381     0    0.280   0.299     6.114   52.500   45.429
LGA    L    33_A      L    33_A     4.012     0    0.643   1.390    10.687   58.333   32.500
LGA    K    34_A      K    34_A     4.029     0    0.603   1.117     8.089   37.619   27.884
LGA    I    35_A      I    35_A     8.453     0    0.014   0.647    12.750    7.262    3.631
LGA    A    36_A      A    36_A     8.009     0    0.031   0.058     9.101   11.548    9.524
LGA    E    37_A      E    37_A     3.013     0    0.068   1.011     7.580   52.262   35.344
LGA    R    38_A      R    38_A     5.178     0    0.000   0.800    16.897   30.476   11.775
LGA    E    39_A      E    39_A     8.115     0    0.055   0.718    15.542   10.357    4.603
LGA    Q    40_A      Q    40_A     6.364     0    0.051   1.181    10.153   21.786   13.122
LGA    G    41_A      G    41_A     2.365     0    0.138   0.138     2.808   62.976   62.976
LGA    E    42_A      E    42_A     3.297     0    0.224   0.657     6.530   46.548   37.513
LGA    G    43_A      G    43_A     5.639     0    0.656   0.656     5.639   30.476   30.476
LGA    E    44_A      E    44_A     1.519     0    0.400   0.685     5.361   68.929   57.196
LGA    F    45_A      F    45_A     1.407     0    0.095   0.523     2.083   79.286   77.576
LGA    D    46_A      D    46_A     1.223     0    0.051   1.139     4.186   81.429   70.774
LGA    E    47_A      E    47_A     1.151     0    0.000   0.678     3.821   83.690   65.503
LGA    C    48_A      C    48_A     1.293     0    0.061   0.888     2.260   81.429   77.222
LGA    L    49_A      L    49_A     0.720     0    0.031   0.995     3.684   95.238   82.619
LGA    E    50_A      E    50_A     0.287     0    0.100   0.722     2.965   92.976   77.831
LGA    A    51_A      A    51_A     1.697     0    0.000   0.028     2.774   69.048   68.190
LGA    L    52_A      L    52_A     3.214     0    0.628   0.937     4.683   48.571   45.298
LGA    D    53_A      D    53_A     3.480     0    0.596   1.191     6.113   46.667   35.298
LGA    D    54_A      D    54_A     7.716     0    0.046   1.076     9.994    8.690    4.702
LGA    A    55_A      A    55_A     9.216     0    0.058   0.073    10.035    4.762    3.810
LGA    K    56_A      K    56_A     3.249     0    0.065   0.922     6.265   32.500   47.619
LGA    R    57_A      R    57_A     7.738     0    0.105   0.766    11.634    7.262    7.186
LGA    A    58_A      A    58_A    12.497     0    0.283   0.292    14.718    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       47     188    188  100.00     365    365  100.00                60
SUMMARY(RMSD_GDC):    10.809         10.436                 11.940           21.546   17.823

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   47   60    4.0     18    2.69    27.917    24.721     0.645

LGA_LOCAL      RMSD:   2.692  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.790  Number of assigned atoms:   47 
Std_ASGN_ATOMS RMSD:  10.809  Standard rmsd on all 47 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.470429 * X  +   0.603595 * Y  +  -0.643715 * Z  + 241.387421
  Y_new =  -0.694029 * X  +  -0.703600 * Y  +  -0.152549 * Z  +  55.254589
  Z_new =  -0.544996 * X  +   0.374993 * Y  +   0.749906 * Z  + -209.684921 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.166483  0.576384  0.463690   [DEG: -124.1304   33.0244   26.5675 ]
ZXZ: -1.338106  0.722876 -0.968125   [DEG:  -76.6678   41.4177  -55.4695 ]
 
# END of job
