
#######################################################
#                                                     #
#                        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        4.54    14.95
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.47    15.21
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.60    15.20
  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    5   13   28   32   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     24   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      6   27   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    3    6   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25      3   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    3   15   17   21   33   37   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25      8   14   14   14   15   15   17   26   31   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   30   33   40   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   30   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   25   27   30   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     13   14   14   14   15   15   17   19   21   22   22   22   22   23   24   27   31   34   36   41 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    4   11   14   15   15   17   19   21   22   22   23   26   30   33   41   43   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   13   16   19   21   22   22   24   29   38   44   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   15   17   19   21   22   22   22   22   41   44   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    9   12   20   32   36   40   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    6    7   27   35   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      4   32   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     31   33   34   36   36   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    4    9   20   36   37   37   38   39   40   41   41   42   42   44   44   44   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     31     33     34     36     36     37     37     38     39     40     41     41     42     42     44     44     44     45     46     46 
GDT PERCENT_AT  53.45  56.90  58.62  62.07  62.07  63.79  63.79  65.52  67.24  68.97  70.69  70.69  72.41  72.41  75.86  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.29   0.40   0.46   0.68   0.68   0.80   0.80   1.33   1.71   2.03   2.32   2.32   2.74   2.74   3.67   3.67   3.67   4.01   4.43   4.43
GDT RMS_ALL_AT  15.22  15.20  15.19  15.22  15.22  15.21  15.21  15.15  15.11  15.03  14.93  14.93  14.90  14.90  14.75  14.75  14.75  14.64  14.53  14.53

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  Y    57_A      Y    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     6.344     0    0.514   0.563     7.870   24.762   21.810
LGA    E     2_A      E     2_A     0.640     0    0.651   1.130     8.381   86.429   51.693
LGA    Y     3_A      Y     3_A     0.542     0    0.016   0.136     0.629   90.476   93.651
LGA    V     4_A      V     4_A     0.421     0    0.029   0.036     0.529  100.000   97.279
LGA    R     5_A      R     5_A     0.260     0    0.023   0.239     2.329  100.000   89.307
LGA    A     6_A      A     6_A     0.300     0    0.051   0.052     0.428  100.000  100.000
LGA    L     7_A      L     7_A     0.399     0    0.043   0.073     0.600   97.619   97.619
LGA    F     8_A      F     8_A     0.649     0    0.032   0.115     0.720   90.476   90.476
LGA    D     9_A      D     9_A     0.721     0    0.058   0.384     2.453   90.476   86.131
LGA    H    10_A      H    10_A     0.793     0    0.020   1.143     2.486   90.476   84.333
LGA    T    11_A      T    11_A     1.366     0    0.647   0.972     3.389   73.571   71.020
LGA    G    12_A      G    12_A     1.367     0    0.091   0.091     1.367   83.690   83.690
LGA    H    13_A      H    13_A     2.341     0    0.629   1.531     4.376   57.857   54.762
LGA    D    14_A      D    14_A     1.639     0    0.101   1.226     5.311   55.952   53.929
LGA    E    15_A      E    15_A     7.202     0    0.713   0.666    14.066   15.357    7.196
LGA    Q    16_A      Q    16_A     8.124     0    0.656   1.213    10.142    4.048    3.492
LGA    E    17_A      E    17_A    11.996     0    0.039   1.020    15.681    0.000    0.000
LGA    L    18_A      L    18_A    19.085     0    0.089   1.357    23.259    0.000    0.000
LGA    P    19_A      P    19_A    24.754     0    0.048   0.339    27.486    0.000    0.000
LGA    F    20_A      F    20_A    30.578     0    0.034   1.451    32.747    0.000    0.000
LGA    K    21_A      K    21_A    37.452     0    0.033   0.084    40.394    0.000    0.000
LGA    K    22_A      K    22_A    40.311     0    0.024   0.506    48.754    0.000    0.000
LGA    G    23_A      G    23_A    42.257     0    0.017   0.017    42.257    0.000    0.000
LGA    E    24_A      E    24_A    38.680     0    0.027   0.999    39.519    0.000    0.000
LGA    I    25_A      I    25_A    36.349     0    0.102   0.640    41.122    0.000    0.000
LGA    L    26_A      L    26_A    29.881     0    0.029   0.079    31.957    0.000    0.000
LGA    R    27_A      R    27_A    28.220     0    0.095   1.324    32.872    0.000    0.000
LGA    I    28_A      I    28_A    21.104     0    0.011   0.069    23.835    0.000    0.000
LGA    R    29_A      R    29_A    20.951     0    0.594   1.208    30.729    0.000    0.000
LGA    D    30_A      D    30_A    16.923     0    0.688   1.037    21.464    0.000    0.000
LGA    K    31_A      K    31_A    14.752     0    0.270   0.272    21.708    0.000    0.000
LGA    P    32_A      P    32_A    13.764     0    0.065   0.363    15.991    0.000    0.000
LGA    E    33_A      E    33_A    10.962     0    0.689   1.050    13.808    0.476    0.212
LGA    E    34_A      E    34_A     7.217     0    0.244   1.087    10.068   15.119    8.201
LGA    Q    35_A      Q    35_A     0.792     0    0.643   0.671     5.308   86.905   68.095
LGA    L    36_A      L    36_A     0.586     0    0.170   1.090     2.568   90.595   79.821
LGA    W    37_A      W    37_A     0.318     0    0.065   0.271     1.584  100.000   90.680
LGA    N    38_A      N    38_A     0.188     0    0.054   0.541     2.149  100.000   89.881
LGA    A    39_A      A    39_A     0.274     0    0.018   0.027     0.361  100.000  100.000
LGA    E    40_A      E    40_A     0.372     0    0.046   0.521     1.903  100.000   94.868
LGA    N    41_A      N    41_A     0.273     0    0.021   0.145     0.622  100.000   98.810
LGA    V    42_A      V    42_A     0.318     0    0.041   1.157     3.185  100.000   86.463
LGA    E    43_A      E    43_A     0.227     0    0.061   0.434     1.621  100.000   90.847
LGA    G    44_A      G    44_A     0.508     0    0.014   0.014     0.580   95.238   95.238
LGA    K    45_A      K    45_A     0.299     0    0.029   0.763     4.515  100.000   78.466
LGA    R    46_A      R    46_A     0.330     0    0.013   0.129     1.352  100.000   90.693
LGA    G    47_A      G    47_A     0.340     0    0.015   0.015     0.340  100.000  100.000
LGA    L    48_A      L    48_A     0.373     0    0.037   0.070     0.540   97.619   97.619
LGA    I    49_A      I    49_A     0.282     0    0.035   0.085     0.353  100.000  100.000
LGA    H    50_A      H    50_A     0.362     0    0.009   0.117     0.689  100.000   97.143
LGA    V    51_A      V    51_A     0.392     0    0.023   0.053     0.504  100.000   98.639
LGA    V    52_A      V    52_A     0.704     0    0.017   0.034     1.008   92.857   90.544
LGA    L    53_A      L    53_A     0.552     0    0.025   0.082     1.189   97.619   91.786
LGA    V    54_A      V    54_A     0.196     0    0.067   0.085     0.474  100.000  100.000
LGA    E    55_A      E    55_A     0.464     0    0.021   0.197     0.820  100.000   97.884
LGA    K    56_A      K    56_A     0.547     0    0.013   0.974     5.125   95.238   77.989
LGA    Y    57_A      Y    57_A     0.501     0    0.576   0.554     2.044   84.048   85.397
LGA    G    58_A      G    58_A     2.909     0    0.302   0.302     4.585   45.714   45.714

# 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):    13.029         12.961                 13.427           59.700   55.886

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.33    65.086    57.199     2.650

LGA_LOCAL      RMSD:   1.334  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.149  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.029  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.821788 * X  +  -0.486505 * Y  +  -0.296612 * Z  + -20.546112
  Y_new =   0.409380 * X  +   0.142045 * Y  +   0.901239 * Z  +  15.278597
  Z_new =  -0.396325 * X  +  -0.862054 * Y  +   0.315896 * Z  + -16.810358 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.462173  0.407510 -1.219547   [DEG:   26.4805   23.3486  -69.8749 ]
ZXZ: -2.823643  1.249396 -2.710665   [DEG: -161.7828   71.5851 -155.3096 ]
 
# END of job
