
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        0.42     0.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.42     0.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.42     0.42
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     60   60   60     31   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     45   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     45   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     46   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     32   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     46   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     45   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     32   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     46   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     36   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     24   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  100.00 )

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     48     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  80.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42
GDT RMS_ALL_AT   0.43   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    50_A      E    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.886     0    0.058   0.720     1.778   90.476   84.940
LGA    D     2_A      D     2_A     0.344     0    0.013   0.464     2.199   97.619   92.024
LGA    K     3_A      K     3_A     0.581     0    0.017   0.554     1.911   90.476   85.503
LGA    A     4_A      A     4_A     0.617     0    0.038   0.047     0.815   95.238   94.286
LGA    A     5_A      A     5_A     0.361     0    0.051   0.067     0.625  100.000   98.095
LGA    C     6_A      C     6_A     0.292     0    0.014   0.049     0.474  100.000  100.000
LGA    A     7_A      A     7_A     0.212     0    0.036   0.041     0.286  100.000  100.000
LGA    D     8_A      D     8_A     0.238     0    0.024   0.108     0.698  100.000   96.429
LGA    G     9_A      G     9_A     0.179     0    0.049   0.049     0.287  100.000  100.000
LGA    I    10_A      I    10_A     0.235     0    0.026   0.046     0.374  100.000  100.000
LGA    A    11_A      A    11_A     0.211     0    0.034   0.046     0.247  100.000  100.000
LGA    A    12_A      A    12_A     0.119     0    0.013   0.018     0.275  100.000  100.000
LGA    V    13_A      V    13_A     0.284     0    0.023   0.051     0.446  100.000  100.000
LGA    K    14_A      K    14_A     0.293     0    0.077   0.154     0.581   97.619   96.825
LGA    A    15_A      A    15_A     0.165     0    0.060   0.056     0.385  100.000  100.000
LGA    R    16_A      R    16_A     0.261     0    0.017   0.161     1.301  100.000   95.714
LGA    V    17_A      V    17_A     0.248     0    0.038   0.051     0.299  100.000  100.000
LGA    E    18_A      E    18_A     0.153     0    0.022   0.804     3.955  100.000   83.810
LGA    K    19_A      K    19_A     0.256     0    0.056   1.061     4.716  100.000   83.704
LGA    L    20_A      L    20_A     0.382     0    0.029   0.170     0.430  100.000  100.000
LGA    A    21_A      A    21_A     0.579     0    0.021   0.040     0.661   90.476   90.476
LGA    P    22_A      P    22_A     0.646     0    0.027   0.047     0.821   90.476   90.476
LGA    E    23_A      E    23_A     0.571     0    0.056   0.934     2.091   92.857   82.804
LGA    A    24_A      A    24_A     0.535     0    0.083   0.094     0.743   92.857   92.381
LGA    V    25_A      V    25_A     0.244     0    0.031   0.064     0.326  100.000  100.000
LGA    P    26_A      P    26_A     0.322     0    0.035   0.089     0.461  100.000  100.000
LGA    Q    27_A      Q    27_A     0.250     0    0.015   1.152     4.460  100.000   84.339
LGA    K    28_A      K    28_A     0.133     0    0.050   0.835     3.645  100.000   80.476
LGA    L    29_A      L    29_A     0.264     0    0.027   1.119     2.755  100.000   89.286
LGA    K    30_A      K    30_A     0.412     0    0.017   0.089     0.672  100.000   98.942
LGA    R    31_A      R    31_A     0.413     0    0.034   1.264     7.087  100.000   68.485
LGA    A    32_A      A    32_A     0.399     0    0.044   0.058     0.456  100.000  100.000
LGA    L    33_A      L    33_A     0.484     0    0.036   0.064     0.609  100.000   98.810
LGA    K    34_A      K    34_A     0.488     0    0.052   0.652     2.752  100.000   90.000
LGA    I    35_A      I    35_A     0.454     0    0.091   0.091     0.623   97.619   98.810
LGA    A    36_A      A    36_A     0.487     0    0.016   0.020     0.570   95.238   96.190
LGA    E    37_A      E    37_A     0.505     0    0.021   0.272     0.759   90.476   93.651
LGA    R    38_A      R    38_A     0.476     0    0.062   0.955     4.169   95.238   79.827
LGA    E    39_A      E    39_A     0.398     0    0.041   1.087     4.051  100.000   83.280
LGA    Q    40_A      Q    40_A     0.474     0    0.075   1.162     4.567   95.238   81.376
LGA    G    41_A      G    41_A     0.350     0    0.048   0.048     0.394  100.000  100.000
LGA    E    42_A      E    42_A     0.416     0    0.140   0.228     1.003   97.619   92.646
LGA    G    43_A      G    43_A     0.308     0    0.048   0.048     0.420  100.000  100.000
LGA    E    44_A      E    44_A     0.351     0    0.054   0.976     4.052  100.000   85.185
LGA    F    45_A      F    45_A     0.535     0    0.011   0.036     0.912   92.857   91.342
LGA    D    46_A      D    46_A     0.644     0    0.070   1.143     4.031   92.857   79.583
LGA    E    47_A      E    47_A     0.472     0    0.031   1.068     3.288   97.619   84.550
LGA    C    48_A      C    48_A     0.149     0    0.020   0.102     0.314  100.000  100.000
LGA    L    49_A      L    49_A     0.266     0    0.036   0.107     0.491  100.000  100.000
LGA    E    50_A      E    50_A     0.169     0    0.026   0.239     1.030  100.000   97.937
LGA    A    51_A      A    51_A     0.091     0    0.013   0.027     0.218  100.000  100.000
LGA    L    52_A      L    52_A     0.290     0    0.015   0.046     0.578  100.000   97.619
LGA    D    53_A      D    53_A     0.282     0    0.026   0.484     2.128  100.000   87.798
LGA    D    54_A      D    54_A     0.191     0    0.015   0.295     1.107  100.000   95.298
LGA    A    55_A      A    55_A     0.396     0    0.014   0.020     0.509   97.619   98.095
LGA    K    56_A      K    56_A     0.679     0    0.043   0.579     1.683   95.238   86.667
LGA    R    57_A      R    57_A     0.293     0    0.016   0.794     2.868  100.000   88.874
LGA    A    58_A      A    58_A     0.578     0    0.035   0.038     0.931   92.857   92.381
LGA    L    59_A      L    59_A     0.483     0    0.043   0.165     1.346   95.238   90.595
LGA    P    60_A      P    60_A     0.945     0    0.030   0.339     1.186   90.476   87.891

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.419          0.415                  1.141           97.738   92.790

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.42   100.000   100.000    11.562

LGA_LOCAL      RMSD:   0.419  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.419  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.419  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.255591 * X  +   0.154843 * Y  +   0.954304 * Z  +  13.668723
  Y_new =  -0.956918 * X  +  -0.181182 * Y  +  -0.226893 * Z  +   6.059741
  Z_new =   0.137770 * X  +  -0.971183 * Y  +   0.194480 * Z  +   7.576902 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.831801 -0.138210 -1.373160   [DEG: -104.9545   -7.9188  -78.6762 ]
ZXZ:  1.337373  1.375069  3.000675   [DEG:   76.6258   78.7856  171.9260 ]
 
# END of job
