
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , 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:    29      30_A - 58_A        4.51    14.85
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.49    15.10
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.77    15.10
  LCS_AVERAGE:     29.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     1_A     A     1_A      3   14   17      3    3    3    4    9   22   29   36   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     24   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     24   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     27   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   15   29   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3   14   32   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    4    6   15   20   24   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25      5   14   14   14   15   15   24   25   30   36   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     10   14   14   14   15   15   16   18   21   22   22   22   26   32   36   40   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   32   37   38 
LCS_GDT     P    19_A     P    19_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   25   29   30   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   29   32   34   37   42 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    4    8   14   15   15   16   18   21   22   22   22   27   32   34   38   45   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   11   15   18   21   22   23   23   27   41   43   44   45   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   12   16   18   21   22   22   22   32   42   43   44   45   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    6    9   13   28   33   38   40   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    3    5    5    5   21   25   37   38   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      5   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     30   34   34   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    6   28   34   35   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_AVERAGE  LCS_A:  35.38  (  29.49   32.82   43.85 )

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     30     34     34     36     36     36     37     37     39     40     41     42     42     42     43     44     45     45     46     46 
GDT PERCENT_AT  51.72  58.62  58.62  62.07  62.07  62.07  63.79  63.79  67.24  68.97  70.69  72.41  72.41  72.41  74.14  75.86  77.59  77.59  79.31  79.31
GDT RMS_LOCAL    0.26   0.36   0.36   0.64   0.64   0.64   0.88   0.88   1.77   2.01   2.33   2.70   2.70   2.70   3.17   3.61   4.07   3.95   4.36   4.36
GDT RMS_ALL_AT  15.11  15.13  15.13  15.16  15.16  15.16  15.14  15.14  15.00  14.96  14.86  14.83  14.83  14.83  14.79  14.70  14.59  14.58  14.47  14.47

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    33_A      E    33_A
#   possible swapping detected:  E    34_A      E    34_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     7.211     0    0.527   0.704     8.980   15.119   13.048
LGA    E     2_A      E     2_A     0.394     0    0.551   1.056     6.341   89.286   57.354
LGA    Y     3_A      Y     3_A     0.267     0    0.073   0.346     2.826  100.000   82.302
LGA    V     4_A      V     4_A     0.353     0    0.029   0.054     0.457  100.000  100.000
LGA    R     5_A      R     5_A     0.423     0    0.016   1.122     3.483  100.000   86.537
LGA    A     6_A      A     6_A     0.533     0    0.021   0.057     0.660   90.476   90.476
LGA    L     7_A      L     7_A     0.574     0    0.070   1.037     2.438   92.857   85.238
LGA    F     8_A      F     8_A     0.489     0    0.000   0.177     0.913   97.619   94.805
LGA    D     9_A      D     9_A     0.602     0    0.021   0.179     0.977   90.476   91.667
LGA    H    10_A      H    10_A     0.641     0    0.028   1.089     2.814   90.476   83.667
LGA    T    11_A      T    11_A     0.640     0    0.651   0.627     2.623   82.143   83.129
LGA    G    12_A      G    12_A     2.126     0    0.115   0.115     2.126   75.238   75.238
LGA    H    13_A      H    13_A     2.195     0    0.632   1.216     4.254   57.857   57.905
LGA    D    14_A      D    14_A     0.857     0    0.021   1.048     5.476   65.595   52.738
LGA    E    15_A      E    15_A     7.096     0    0.661   0.811    13.873   16.071    7.513
LGA    Q    16_A      Q    16_A     8.547     0    0.671   1.013    10.514    2.619    2.275
LGA    E    17_A      E    17_A    12.061     0    0.057   0.899    15.844    0.000    0.000
LGA    L    18_A      L    18_A    19.202     0    0.077   1.011    22.988    0.000    0.000
LGA    P    19_A      P    19_A    24.618     0    0.067   0.121    27.377    0.000    0.000
LGA    F    20_A      F    20_A    30.421     0    0.038   1.441    32.523    0.000    0.000
LGA    K    21_A      K    21_A    37.174     0    0.032   0.773    43.390    0.000    0.000
LGA    K    22_A      K    22_A    40.281     0    0.000   0.549    48.877    0.000    0.000
LGA    G    23_A      G    23_A    42.304     0    0.050   0.050    42.304    0.000    0.000
LGA    E    24_A      E    24_A    38.649     0    0.000   1.027    39.434    0.000    0.000
LGA    I    25_A      I    25_A    36.343     0    0.000   0.602    41.183    0.000    0.000
LGA    L    26_A      L    26_A    29.982     0    0.023   0.041    31.986    0.000    0.000
LGA    R    27_A      R    27_A    28.243     0    0.044   0.092    32.297    0.000    0.000
LGA    I    28_A      I    28_A    21.162     0    0.518   0.918    23.876    0.000    0.000
LGA    R    29_A      R    29_A    20.954     0    0.600   1.193    28.015    0.000    0.000
LGA    D    30_A      D    30_A    16.990     0    0.663   1.083    20.811    0.000    0.000
LGA    K    31_A      K    31_A    14.964     0    0.315   0.343    21.876    0.000    0.000
LGA    P    32_A      P    32_A    13.697     0    0.132   0.395    16.073    0.000    0.000
LGA    E    33_A      E    33_A    10.704     0    0.699   1.058    13.340    0.476    0.212
LGA    E    34_A      E    34_A     6.805     0    0.193   0.963     8.270   19.048   14.974
LGA    Q    35_A      Q    35_A     0.872     0    0.649   1.233     5.139   84.524   63.175
LGA    L    36_A      L    36_A     0.548     0    0.137   0.712     1.685   90.595   87.202
LGA    W    37_A      W    37_A     0.444     0    0.027   0.233     1.494  100.000   91.293
LGA    N    38_A      N    38_A     0.498     0    0.029   0.907     2.991   97.619   85.536
LGA    A    39_A      A    39_A     0.095     0    0.000   0.000     0.431  100.000  100.000
LGA    E    40_A      E    40_A     0.051     0    0.026   0.191     0.960  100.000   97.884
LGA    N    41_A      N    41_A     0.042     0    0.023   0.337     1.595  100.000   96.607
LGA    V    42_A      V    42_A     0.237     0    0.079   0.079     0.577  100.000   98.639
LGA    E    43_A      E    43_A     0.181     0    0.068   0.358     1.167  100.000   94.815
LGA    G    44_A      G    44_A     0.269     0    0.063   0.063     0.358  100.000  100.000
LGA    K    45_A      K    45_A     0.275     0    0.000   0.931     4.782  100.000   76.614
LGA    R    46_A      R    46_A     0.157     0    0.055   0.110     0.229  100.000  100.000
LGA    G    47_A      G    47_A     0.201     0    0.036   0.036     0.220  100.000  100.000
LGA    L    48_A      L    48_A     0.306     0    0.000   0.235     1.092  100.000   95.298
LGA    I    49_A      I    49_A     0.413     0    0.037   0.080     0.502  100.000   98.810
LGA    H    50_A      H    50_A     0.462     0    0.000   1.307     6.549  100.000   67.571
LGA    V    51_A      V    51_A     0.403     0    0.000   0.035     0.519  100.000   98.639
LGA    V    52_A      V    52_A     0.305     0    0.021   0.088     0.604  100.000   98.639
LGA    L    53_A      L    53_A     0.295     0    0.044   0.921     2.347  100.000   91.012
LGA    V    54_A      V    54_A     0.281     0    0.054   0.091     0.413  100.000  100.000
LGA    E    55_A      E    55_A     0.118     0    0.000   0.535     2.209  100.000   89.947
LGA    K    56_A      K    56_A     0.337     0    0.083   0.976     4.096  100.000   79.048
LGA    Y    57_A      Y    57_A     0.592     0    0.187   0.365     3.090   81.786   70.675
LGA    G    58_A      G    58_A     3.571     0    0.548   0.548     5.017   41.429   41.429

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    12.997         12.924                 13.397           60.023   55.205

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.88    65.086    57.184     3.781

LGA_LOCAL      RMSD:   0.879  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.145  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  12.997  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.429915 * X  +   0.788119 * Y  +   0.440502 * Z  + 180.410934
  Y_new =   0.731318 * X  +   0.590088 * Y  +  -0.342009 * Z  + -322.737366
  Z_new =  -0.529479 * X  +   0.175112 * Y  +  -0.830053 * Z  + 213.334015 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.102244  0.557986  2.933676   [DEG:  120.4497   31.9703  168.0872 ]
ZXZ:  0.910608  2.549999 -1.251394   [DEG:   52.1740  146.1042  -71.6996 ]
 
# END of job
