
#######################################################
#                                                     #
#                        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   57 (  477),  selected   57 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   57 , 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:    28      30_A - 57_A        4.58    15.05
  LCS_AVERAGE:     42.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      34_A - 57_A        1.40    15.28
  LCS_AVERAGE:     32.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      35_A - 57_A        0.28    15.29
  LCS_AVERAGE:     28.58

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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   10   14   29   34   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     E     2_A     E     2_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     V     4_A     V     4_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     R     5_A     R     5_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     A     6_A     A     6_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     L     7_A     L     7_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     F     8_A     F     8_A     13   14   17     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     D     9_A     D     9_A     13   14   17     24   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     H    10_A     H    10_A     13   14   17     24   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     T    11_A     T    11_A     13   14   17     24   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     G    12_A     G    12_A     13   14   22      4   29   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     H    13_A     H    13_A     13   14   25      4    6   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     D    14_A     D    14_A     13   17   25     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     E    15_A     E    15_A      3   17   25      3    3    3    5    7   20   26   33   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     Q    16_A     Q    16_A     15   17   25      6   14   14   14   15   15   24   26   27   35   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     E    17_A     E    17_A     15   17   25     11   14   14   14   15   15   16   18   20   22   22   22   25   30   36   40   42   44   45   45 
LCS_GDT     L    18_A     L    18_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   31   34   36 
LCS_GDT     P    19_A     P    19_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     F    20_A     F    20_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     K    21_A     K    21_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   29   29 
LCS_GDT     K    22_A     K    22_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   29   29 
LCS_GDT     G    23_A     G    23_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     E    24_A     E    24_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     I    25_A     I    25_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     L    26_A     L    26_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     R    27_A     R    27_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   26   28   29   29 
LCS_GDT     I    28_A     I    28_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   23   25   29   30   34   35 
LCS_GDT     R    29_A     R    29_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   29   30   33   34   37 
LCS_GDT     D    30_A     D    30_A     15   17   28      3    5    8   14   15   15   16   18   20   22   22   24   27   30   32   34   42   44   45   45 
LCS_GDT     K    31_A     K    31_A      4   16   28      3    3    4    5    7   11   15   18   20   22   23   24   27   37   42   43   43   44   45   45 
LCS_GDT     P    32_A     P    32_A      4    6   28      3    3    4    5    7   11   16   18   20   22   22   23   40   40   42   43   43   44   45   45 
LCS_GDT     E    33_A     E    33_A      4    5   28      3    3    4    5    6    8   11   24   31   36   39   40   41   41   42   43   43   44   45   45 
LCS_GDT     E    34_A     E    34_A      4   24   28      3    3    4    4    6   10   25   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     Q    35_A     Q    35_A     23   24   28     16   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     L    36_A     L    36_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     W    37_A     W    37_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     N    38_A     N    38_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     A    39_A     A    39_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     E    40_A     E    40_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     N    41_A     N    41_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     V    42_A     V    42_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     E    43_A     E    43_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     G    44_A     G    44_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     K    45_A     K    45_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     R    46_A     R    46_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     G    47_A     G    47_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     L    48_A     L    48_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     I    49_A     I    49_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     H    50_A     H    50_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     V    51_A     V    51_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     V    52_A     V    52_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     L    53_A     L    53_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     V    54_A     V    54_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     E    55_A     E    55_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     K    56_A     K    56_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_GDT     Y    57_A     Y    57_A     23   24   28     29   34   35   36   36   36   36   36   37   38   40   40   41   41   42   43   43   44   45   45 
LCS_AVERAGE  LCS_A:  34.65  (  28.58   32.49   42.89 )

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     29     34     35     36     36     36     36     36     37     38     40     40     41     41     42     43     43     44     45     45 
GDT PERCENT_AT  50.00  58.62  60.34  62.07  62.07  62.07  62.07  62.07  63.79  65.52  68.97  68.97  70.69  70.69  72.41  74.14  74.14  75.86  77.59  77.59
GDT RMS_LOCAL    0.21   0.37   0.50   0.61   0.61   0.61   0.61   0.61   1.25   1.63   2.33   2.33   2.71   2.71   3.18   3.63   3.63   3.98   4.40   4.40
GDT RMS_ALL_AT  15.28  15.30  15.32  15.34  15.34  15.34  15.34  15.34  15.29  15.24  15.05  15.05  15.02  15.02  14.98  14.89  14.89  14.77  14.66  14.66

# 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:  D    14_A      D    14_A
#   possible swapping detected:  D    30_A      D    30_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     7.322     0    0.522   0.598     8.765   17.619   15.048
LGA    E     2_A      E     2_A     0.162     0    0.656   1.015     6.762   89.286   60.053
LGA    Y     3_A      Y     3_A     0.205     0    0.022   0.168     1.403  100.000   92.183
LGA    V     4_A      V     4_A     0.095     0    0.025   0.049     0.136  100.000  100.000
LGA    R     5_A      R     5_A     0.149     0    0.018   1.129     4.459  100.000   85.281
LGA    A     6_A      A     6_A     0.149     0    0.075   0.075     0.303  100.000  100.000
LGA    L     7_A      L     7_A     0.102     0    0.022   0.078     0.353  100.000  100.000
LGA    F     8_A      F     8_A     0.309     0    0.021   0.111     0.487  100.000  100.000
LGA    D     9_A      D     9_A     0.674     0    0.051   0.259     1.173   90.476   89.345
LGA    H    10_A      H    10_A     0.774     0    0.022   1.095     2.698   90.476   82.714
LGA    T    11_A      T    11_A     0.635     0    0.638   0.963     2.722   82.143   77.279
LGA    G    12_A      G    12_A     1.775     0    0.075   0.075     1.775   75.000   75.000
LGA    H    13_A      H    13_A     2.034     0    0.641   1.246     4.615   59.881   55.857
LGA    D    14_A      D    14_A     1.008     0    0.046   0.994     5.269   60.357   53.393
LGA    E    15_A      E    15_A     7.375     0    0.704   0.663    14.639   13.929    6.349
LGA    Q    16_A      Q    16_A     8.623     0    0.650   1.388    13.622    2.619    1.640
LGA    E    17_A      E    17_A    12.112     0    0.059   1.063    15.837    0.000    0.000
LGA    L    18_A      L    18_A    19.290     0    0.080   1.367    23.577    0.000    0.000
LGA    P    19_A      P    19_A    24.707     0    0.032   0.337    27.619    0.000    0.000
LGA    F    20_A      F    20_A    30.529     0    0.020   1.444    32.582    0.000    0.000
LGA    K    21_A      K    21_A    37.234     0    0.017   0.708    42.056    0.000    0.000
LGA    K    22_A      K    22_A    40.254     0    0.080   0.532    48.545    0.000    0.000
LGA    G    23_A      G    23_A    42.370     0    0.047   0.047    42.370    0.000    0.000
LGA    E    24_A      E    24_A    38.698     0    0.042   1.031    39.559    0.000    0.000
LGA    I    25_A      I    25_A    36.562     0    0.081   0.634    41.313    0.000    0.000
LGA    L    26_A      L    26_A    30.217     0    0.010   0.057    32.222    0.000    0.000
LGA    R    27_A      R    27_A    28.576     0    0.094   1.362    33.539    0.000    0.000
LGA    I    28_A      I    28_A    21.496     0    0.015   0.074    24.201    0.000    0.000
LGA    R    29_A      R    29_A    21.264     0    0.587   1.144    30.940    0.000    0.000
LGA    D    30_A      D    30_A    17.140     0    0.663   1.046    21.759    0.000    0.000
LGA    K    31_A      K    31_A    14.981     0    0.279   0.339    22.847    0.000    0.000
LGA    P    32_A      P    32_A    13.585     0    0.084   0.358    15.938    0.000    0.000
LGA    E    33_A      E    33_A    10.782     0    0.692   1.075    13.882    0.476    0.212
LGA    E    34_A      E    34_A     7.020     0    0.139   0.891    10.564   17.500    8.942
LGA    Q    35_A      Q    35_A     0.872     0    0.642   0.770     5.760   86.905   64.339
LGA    L    36_A      L    36_A     0.308     0    0.129   1.131     3.189   95.238   83.393
LGA    W    37_A      W    37_A     0.261     0    0.021   0.180     1.178  100.000   95.306
LGA    N    38_A      N    38_A     0.294     0    0.028   0.568     2.326  100.000   89.881
LGA    A    39_A      A    39_A     0.217     0    0.013   0.020     0.416  100.000  100.000
LGA    E    40_A      E    40_A     0.287     0    0.025   0.659     2.186  100.000   92.910
LGA    N    41_A      N    41_A     0.172     0    0.010   0.082     0.631  100.000   98.810
LGA    V    42_A      V    42_A     0.326     0    0.051   1.156     2.953  100.000   88.639
LGA    E    43_A      E    43_A     0.319     0    0.040   0.405     1.346   97.619   94.762
LGA    G    44_A      G    44_A     0.459     0    0.011   0.011     0.556   97.619   97.619
LGA    K    45_A      K    45_A     0.416     0    0.035   0.787     5.098  100.000   76.349
LGA    R    46_A      R    46_A     0.234     0    0.020   0.218     0.921  100.000   95.671
LGA    G    47_A      G    47_A     0.309     0    0.028   0.028     0.309  100.000  100.000
LGA    L    48_A      L    48_A     0.253     0    0.052   0.168     0.814  100.000   98.810
LGA    I    49_A      I    49_A     0.350     0    0.094   0.129     0.545   97.619   97.619
LGA    H    50_A      H    50_A     0.559     0    0.036   0.188     1.571   92.857   85.190
LGA    V    51_A      V    51_A     0.483     0    0.023   0.078     0.559   97.619   95.918
LGA    V    52_A      V    52_A     0.516     0    0.013   0.032     0.863   97.619   94.558
LGA    L    53_A      L    53_A     0.371     0    0.018   0.081     0.781  100.000   98.810
LGA    V    54_A      V    54_A     0.262     0    0.123   0.171     0.725   97.619   97.279
LGA    E    55_A      E    55_A     0.146     0    0.006   0.064     0.442  100.000  100.000
LGA    K    56_A      K    56_A     0.171     0    0.021   0.588     1.296  100.000   93.757
LGA    Y    57_A      Y    57_A     0.184     0    0.560   0.528     2.534   89.286   90.952

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     477    477  100.00                58
SUMMARY(RMSD_GDC):    13.169         13.098                 13.520           59.479   55.756

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57   58    4.0     36    0.61    64.224    56.299     5.105

LGA_LOCAL      RMSD:   0.605  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.336  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  13.169  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.450419 * X  +   0.891258 * Y  +   0.052736 * Z  + -54.331856
  Y_new =   0.867043 * X  +  -0.450743 * Y  +   0.212293 * Z  +  45.711212
  Z_new =   0.212978 * X  +  -0.049896 * Y  +  -0.975782 * Z  +  -0.765637 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.091679 -0.214622 -3.090503   [DEG:   62.5486  -12.2969 -177.0728 ]
ZXZ:  2.898108  2.921065  1.800924   [DEG:  166.0493  167.3647  103.1853 ]
 
# END of job
