
#######################################################
#                                                     #
#                        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        4.53    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        1.43    15.19
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.53    15.19
  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    6   13   22   35   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     28   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   25   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    5   28   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25     13   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    5   10   14   15   27   31   36   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25      6   14   14   14   15   15   17   26   29   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   24   31   35   40   42   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   27   29   34   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   29   33   34   36   41 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    5   12   14   15   15   16   19   20   22   22   22   26   30   34   40   42   44   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   15   19   20   22   22   27   28   33   42   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   13   16   19   20   22   22   22   25   38   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    8   11   24   30   37   40   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    5    9   24   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      4   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    5   15   36   37   37   37   38   39   40   41   41   42   42   43   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     37     37     37     38     39     40     41     41     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  53.45  56.90  58.62  62.07  63.79  63.79  63.79  65.52  67.24  68.97  70.69  70.69  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.24   0.31   0.39   0.62   0.72   0.72   0.72   1.27   1.63   2.05   2.28   2.28   2.69   2.69   3.17   3.62   3.62   3.97   4.39   4.39
GDT RMS_ALL_AT  15.22  15.21  15.19  15.22  15.21  15.21  15.21  15.15  15.12  14.96  14.93  14.93  14.90  14.90  14.86  14.76  14.76  14.65  14.54  14.54

# Checking swapping
#   possible swapping detected:  E     2_A      E     2_A
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_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     6.216     0    0.517   0.566     7.716   24.762   21.810
LGA    E     2_A      E     2_A     0.695     0    0.648   1.167     7.672   86.429   49.524
LGA    Y     3_A      Y     3_A     0.443     0    0.009   0.130     0.670  100.000   96.825
LGA    V     4_A      V     4_A     0.366     0    0.045   0.053     0.478  100.000  100.000
LGA    R     5_A      R     5_A     0.254     0    0.023   0.182     1.921  100.000   92.424
LGA    A     6_A      A     6_A     0.244     0    0.055   0.059     0.370  100.000  100.000
LGA    L     7_A      L     7_A     0.238     0    0.060   0.078     0.455  100.000  100.000
LGA    F     8_A      F     8_A     0.395     0    0.025   0.117     0.438  100.000  100.000
LGA    D     9_A      D     9_A     0.501     0    0.055   0.378     2.176   92.857   88.512
LGA    H    10_A      H    10_A     0.597     0    0.018   1.141     2.594   90.476   84.571
LGA    T    11_A      T    11_A     1.061     0    0.655   0.925     3.182   75.833   74.626
LGA    G    12_A      G    12_A     1.488     0    0.088   0.088     1.488   83.690   83.690
LGA    H    13_A      H    13_A     2.099     0    0.635   1.319     4.182   61.905   57.905
LGA    D    14_A      D    14_A     1.641     0    0.102   1.229     5.400   58.214   55.060
LGA    E    15_A      E    15_A     7.420     0    0.709   0.610    14.269   14.643    6.878
LGA    Q    16_A      Q    16_A     8.244     0    0.655   1.259    10.154    3.333    2.857
LGA    E    17_A      E    17_A    12.018     0    0.042   1.005    15.712    0.000    0.000
LGA    L    18_A      L    18_A    19.142     0    0.101   1.360    23.326    0.000    0.000
LGA    P    19_A      P    19_A    24.731     0    0.052   0.325    27.547    0.000    0.000
LGA    F    20_A      F    20_A    30.576     0    0.043   1.450    32.716    0.000    0.000
LGA    K    21_A      K    21_A    37.440     0    0.033   0.112    40.050    0.000    0.000
LGA    K    22_A      K    22_A    40.327     0    0.027   0.494    48.859    0.000    0.000
LGA    G    23_A      G    23_A    42.326     0    0.021   0.021    42.326    0.000    0.000
LGA    E    24_A      E    24_A    38.693     0    0.028   1.008    39.550    0.000    0.000
LGA    I    25_A      I    25_A    36.389     0    0.092   0.627    41.199    0.000    0.000
LGA    L    26_A      L    26_A    29.945     0    0.036   0.081    32.009    0.000    0.000
LGA    R    27_A      R    27_A    28.335     0    0.095   1.177    32.745    0.000    0.000
LGA    I    28_A      I    28_A    21.186     0    0.012   0.062    23.926    0.000    0.000
LGA    R    29_A      R    29_A    20.938     0    0.591   1.201    30.771    0.000    0.000
LGA    D    30_A      D    30_A    16.881     0    0.688   0.842    21.236    0.000    0.000
LGA    K    31_A      K    31_A    14.672     0    0.272   0.279    21.576    0.000    0.000
LGA    P    32_A      P    32_A    13.509     0    0.068   0.368    15.806    0.000    0.000
LGA    E    33_A      E    33_A    10.684     0    0.686   1.054    13.734    1.071    0.476
LGA    E    34_A      E    34_A     6.884     0    0.191   0.992    10.280   19.048   10.106
LGA    Q    35_A      Q    35_A     0.701     0    0.661   0.674     5.608   86.905   65.026
LGA    L    36_A      L    36_A     0.621     0    0.162   0.566     1.398   90.595   88.274
LGA    W    37_A      W    37_A     0.356     0    0.060   0.277     1.619  100.000   90.000
LGA    N    38_A      N    38_A     0.295     0    0.040   0.413     1.660  100.000   93.095
LGA    A    39_A      A    39_A     0.300     0    0.010   0.028     0.350  100.000  100.000
LGA    E    40_A      E    40_A     0.365     0    0.046   0.697     1.877  100.000   92.910
LGA    N    41_A      N    41_A     0.252     0    0.026   0.156     0.836  100.000   98.810
LGA    V    42_A      V    42_A     0.454     0    0.035   1.142     3.224  100.000   87.619
LGA    E    43_A      E    43_A     0.206     0    0.057   0.424     1.482  100.000   93.757
LGA    G    44_A      G    44_A     0.532     0    0.013   0.013     0.609   95.238   95.238
LGA    K    45_A      K    45_A     0.354     0    0.026   0.759     4.615  100.000   77.566
LGA    R    46_A      R    46_A     0.360     0    0.016   0.157     1.382  100.000   89.827
LGA    G    47_A      G    47_A     0.366     0    0.012   0.012     0.366  100.000  100.000
LGA    L    48_A      L    48_A     0.368     0    0.042   0.077     0.732  100.000   98.810
LGA    I    49_A      I    49_A     0.206     0    0.033   0.069     0.267  100.000  100.000
LGA    H    50_A      H    50_A     0.354     0    0.022   0.106     0.848  100.000   96.190
LGA    V    51_A      V    51_A     0.396     0    0.026   0.040     0.428  100.000  100.000
LGA    V    52_A      V    52_A     0.659     0    0.014   0.059     0.938   92.857   91.837
LGA    L    53_A      L    53_A     0.498     0    0.029   0.078     0.962  100.000   95.238
LGA    V    54_A      V    54_A     0.207     0    0.082   0.096     0.450  100.000  100.000
LGA    E    55_A      E    55_A     0.415     0    0.026   0.242     0.799  100.000   98.942
LGA    K    56_A      K    56_A     0.461     0    0.021   0.592     1.457  100.000   93.704
LGA    Y    57_A      Y    57_A     0.471     0    0.573   0.564     2.130   91.190   88.571
LGA    G    58_A      G    58_A     2.497     0    0.660   0.660     3.483   57.381   57.381

# 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):    13.050         12.986                 13.443           60.800   57.208

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.27    65.086    57.274     2.777

LGA_LOCAL      RMSD:   1.269  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.151  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.050  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.614250 * X  +   0.181475 * Y  +  -0.767961 * Z  + -21.310110
  Y_new =  -0.777158 * X  +  -0.307870 * Y  +   0.548854 * Z  +  16.929798
  Z_new =  -0.136829 * X  +   0.933961 * Y  +   0.330144 * Z  + -16.556736 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.239644  0.137259  1.231018   [DEG: -128.3221    7.8644   70.5321 ]
ZXZ: -2.191314  1.234340 -0.145469   [DEG: -125.5530   70.7225   -8.3347 ]
 
# END of job
