
#######################################################
#                                                     #
#                        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   53 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.45     1.45
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.45     1.45
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        0.97     1.46
  LONGEST_CONTINUOUS_SEGMENT:    46       3_F - 48_F        0.99     1.50
  LONGEST_CONTINUOUS_SEGMENT:    46       4_F - 49_F        0.98     1.54
  LCS_AVERAGE:     92.17

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F      5   49   49      3    4    8    8   22   35   41   44   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     46   49   49      5   19   40   43   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      5   25   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     20   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     20   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     14   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49      5   32   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     17   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     19   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     15   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     17   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49      3    6   31   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49      3   10   23   43   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49      3   37   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49     12   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49     18   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     18   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49     18   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49     20   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49     20   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     19   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     46   49   49      4   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     46   49   49     19   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     20   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     21   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49      4   23   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49     15   38   42   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     46   49   49      3    3   19   40   45   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F     46   49   49      0    0    3   45   47   48   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  97.39  (  92.17  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     21     38     42     45     47     48     48     48     48     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  42.86  77.55  85.71  91.84  95.92  97.96  97.96  97.96  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.55   0.67   0.84   1.01   1.12   1.12   1.12   1.12   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45
GDT RMS_ALL_AT   1.53   1.49   1.50   1.49   1.46   1.48   1.48   1.48   1.48   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45

# Checking swapping
#   possible swapping detected:  D    11_F      D    11_F
#   possible swapping detected:  E    40_F      E    40_F
#   possible swapping detected:  E    47_F      E    47_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F     6.883     0    0.095   1.131     8.219   17.024   15.893
LGA    G     2_F      G     2_F     3.087     0    0.107   0.107     4.494   48.571   48.571
LGA    K     3_F      K     3_F     1.917     0    0.026   1.052     5.649   77.381   58.783
LGA    I     4_F      I     4_F     0.555     0    0.090   0.148     0.872   95.238   95.238
LGA    K     5_F      K     5_F     0.576     0    0.043   0.674     2.723   92.857   78.413
LGA    R     6_F      R     6_F     0.127     0    0.017   1.462     6.548  100.000   75.844
LGA    F     7_F      F     7_F     0.338     0    0.028   0.049     0.517   97.619   99.134
LGA    F     8_F      F     8_F     0.637     0    0.032   0.355     1.173   90.476   88.874
LGA    A     9_F      A     9_F     0.551     0    0.071   0.091     0.878   90.476   92.381
LGA    K    10_F      K    10_F     0.912     0    0.043   1.027     5.769   92.857   71.481
LGA    D    11_F      D    11_F     1.187     0    0.096   0.946     3.418   90.595   78.869
LGA    M    12_F      M    12_F     0.665     0    0.035   1.071     4.473   95.238   82.976
LGA    R    13_F      R    13_F     0.693     0    0.049   1.923    10.298   90.476   51.732
LGA    A    14_F      A    14_F     0.614     0    0.028   0.030     0.667   90.476   90.476
LGA    A    15_F      A    15_F     0.391     0    0.044   0.045     0.452  100.000  100.000
LGA    L    16_F      L    16_F     0.442     0    0.011   1.112     3.007   97.619   85.655
LGA    A    17_F      A    17_F     0.790     0    0.029   0.032     0.934   90.476   90.476
LGA    Q    18_F      Q    18_F     0.655     0    0.027   0.352     1.054   92.857   93.704
LGA    V    19_F      V    19_F     0.428     0    0.012   0.079     0.532   97.619   98.639
LGA    K    20_F      K    20_F     0.741     0    0.022   1.442     7.697   90.476   63.810
LGA    D    21_F      D    21_F     0.746     0    0.012   0.851     3.858   90.476   75.357
LGA    T    22_F      T    22_F     0.583     0    0.097   1.129     2.229   95.238   87.007
LGA    L    23_F      L    23_F     0.502     0    0.188   1.104     2.723   92.857   84.286
LGA    G    24_F      G    24_F     2.023     0    0.424   0.424     3.528   61.429   61.429
LGA    S    25_F      S    25_F     2.687     0    0.628   0.578     5.090   49.524   49.683
LGA    D    26_F      D    26_F     1.262     0    0.353   0.829     3.330   81.548   70.476
LGA    A    27_F      A    27_F     0.730     0    0.112   0.162     0.977   90.476   90.476
LGA    V    28_F      V    28_F     0.584     0    0.048   0.087     0.970   97.619   94.558
LGA    I    29_F      I    29_F     0.342     0    0.059   0.657     2.453  100.000   94.405
LGA    M    30_F      M    30_F     0.430     0    0.024   0.147     0.454  100.000  100.000
LGA    S    31_F      S    31_F     0.406     0    0.061   0.510     2.729   97.619   89.683
LGA    N    32_F      N    32_F     0.999     0    0.399   1.250     4.201   84.167   74.107
LGA    K    33_F      K    33_F     1.099     0    0.149   1.018     4.137   79.286   71.005
LGA    K    34_F      K    34_F     1.103     0    0.219   0.672     2.757   83.690   76.931
LGA    V    35_F      V    35_F     0.579     0    0.228   0.915     2.558   86.071   79.524
LGA    N    36_F      N    36_F     0.584     0    0.385   1.357     3.234   82.738   80.179
LGA    G    37_F      G    37_F     0.302     0    0.184   0.184     2.177   86.429   86.429
LGA    G    38_F      G    38_F     0.293     0    0.075   0.075     0.304  100.000  100.000
LGA    I    39_F      I    39_F     0.284     0    0.078   1.022     2.362   97.619   85.595
LGA    E    40_F      E    40_F     0.609     0    0.129   0.816     2.500   88.214   78.095
LGA    I    41_F      I    41_F     0.549     0    0.042   1.259     2.923   95.238   84.286
LGA    V    42_F      V    42_F     0.256     0    0.026   1.160     2.601  100.000   87.483
LGA    A    43_F      A    43_F     0.203     0    0.083   0.103     0.300  100.000  100.000
LGA    A    44_F      A    44_F     0.500     0    0.026   0.031     0.898   95.238   94.286
LGA    V    45_F      V    45_F     0.403     0    0.054   1.243     3.167   95.238   84.898
LGA    L    46_F      L    46_F     1.723     0    0.583   1.160     4.274   67.619   56.607
LGA    E    47_F      E    47_F     0.878     0    0.189   0.886     2.944   92.857   80.952
LGA    H    48_F      H    48_F     3.214     0    0.559   1.242     8.791   55.714   29.810
LGA    H    49_F      H    49_F     2.077     0    0.644   0.748     9.233   61.071   32.143

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):     1.447          1.529                  2.554           86.659   78.380

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     48    1.12    91.837    95.874     3.950

LGA_LOCAL      RMSD:   1.115  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.478  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.447  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.158806 * X  +  -0.969215 * Y  +   0.188158 * Z  +  65.761581
  Y_new =   0.042900 * X  +  -0.183623 * Y  +  -0.982060 * Z  + -79.618011
  Z_new =   0.986377 * X  +   0.164029 * Y  +   0.012419 * Z  + -19.479445 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.263842 -1.405547  1.495230   [DEG:   15.1170  -80.5319   85.6704 ]
ZXZ:  0.189301  1.558377  1.406010   [DEG:   10.8462   89.2884   80.5584 ]
 
# END of job
