
#######################################################
#                                                     #
#                        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   50 (  401),  selected   50 , name one
# Molecule2: number of CA atoms   97 (  780),  selected   50 , 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:    50      50_A - 99_A        1.05     1.05
  LCS_AVERAGE:     51.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50      50_A - 99_A        1.05     1.05
  LCS_AVERAGE:     51.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      51_A - 99_A        0.71     1.07
  LCS_AVERAGE:     49.57

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   50
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     G    50_A     G    50_A      3   50   50      3    3    3   12   24   33   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     G    51_A     G    51_A     49   50   50      3    7   29   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     G    52_A     G    52_A     49   50   50      4   23   45   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     E    53_A     E    53_A     49   50   50      4   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     W    54_A     W    54_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     E    55_A     E    55_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     I    56_A     I    56_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     I    57_A     I    57_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     D    58_A     D    58_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     I    59_A     I    59_A     49   50   50      6   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     G    60_A     G    60_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     P    61_A     P    61_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     F    62_A     F    62_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     T    63_A     T    63_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     Q    64_A     Q    64_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     N    65_A     N    65_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     L    66_A     L    66_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     G    67_A     G    67_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     K    68_A     K    68_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     F    69_A     F    69_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     A    70_A     A    70_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     V    71_A     V    71_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     D    72_A     D    72_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     E    73_A     E    73_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     E    74_A     E    74_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     N    75_A     N    75_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     K    76_A     K    76_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     I    77_A     I    77_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     G    78_A     G    78_A     49   50   50     20   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     Q    79_A     Q    79_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     Y    80_A     Y    80_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     G    81_A     G    81_A     49   50   50     20   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     R    82_A     R    82_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     L    83_A     L    83_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     T    84_A     T    84_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     F    85_A     F    85_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     N    86_A     N    86_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     K    87_A     K    87_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     V    88_A     V    88_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     I    89_A     I    89_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     R    90_A     R    90_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     P    91_A     P    91_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     C    92_A     C    92_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     M    93_A     M    93_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     K    94_A     K    94_A     49   50   50     38   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     K    95_A     K    95_A     49   50   50     32   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     T    96_A     T    96_A     49   50   50     32   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     I    97_A     I    97_A     49   50   50     32   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     Y    98_A     Y    98_A     49   50   50      6   45   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_GDT     E    99_A     E    99_A     49   50   50      5   24   47   49   49   49   50   50   50   50   50   50   50   50   50   50   50   50   50   50 
LCS_AVERAGE  LCS_A:  50.89  (  49.57   51.55   51.55 )

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     38     45     47     49     49     49     50     50     50     50     50     50     50     50     50     50     50     50     50     50 
GDT PERCENT_AT  39.18  46.39  48.45  50.52  50.52  50.52  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55  51.55
GDT RMS_LOCAL    0.29   0.41   0.48   0.71   0.71   0.71   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05
GDT RMS_ALL_AT   1.22   1.13   1.12   1.07   1.07   1.07   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05

# Checking swapping
#   possible swapping detected:  E    53_A      E    53_A
#   possible swapping detected:  F    62_A      F    62_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  Y    80_A      Y    80_A
#   possible swapping detected:  Y    98_A      Y    98_A
#   possible swapping detected:  E    99_A      E    99_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    50_A      G    50_A     5.369     0    0.049   0.049     6.544   24.524   24.524
LGA    G    51_A      G    51_A     2.318     0    0.078   0.078     3.295   59.167   59.167
LGA    G    52_A      G    52_A     2.128     0    0.022   0.022     2.465   73.095   73.095
LGA    E    53_A      E    53_A     1.133     0    0.022   0.792     4.207   83.690   69.259
LGA    W    54_A      W    54_A     0.634     0    0.020   0.079     0.841   90.476   91.837
LGA    E    55_A      E    55_A     0.499     0    0.011   0.852     3.117  100.000   88.201
LGA    I    56_A      I    56_A     0.425     0    0.021   0.627     1.871  100.000   94.226
LGA    I    57_A      I    57_A     0.314     0    0.044   0.092     0.507   97.619   98.810
LGA    D    58_A      D    58_A     0.494     0    0.049   0.593     3.215   97.619   82.560
LGA    I    59_A      I    59_A     0.627     0    0.487   1.441     3.537   78.095   72.024
LGA    G    60_A      G    60_A     0.207     0    0.058   0.058     0.472  100.000  100.000
LGA    P    61_A      P    61_A     0.758     0    0.053   0.052     1.225   90.476   87.891
LGA    F    62_A      F    62_A     0.876     0    0.022   0.104     1.404   90.476   84.719
LGA    T    63_A      T    63_A     0.520     0    0.009   1.117     2.408   95.238   85.850
LGA    Q    64_A      Q    64_A     0.173     0    0.015   0.199     1.015  100.000   95.820
LGA    N    65_A      N    65_A     0.655     0    0.023   0.173     1.191   90.476   89.345
LGA    L    66_A      L    66_A     0.683     0    0.015   0.200     1.033   92.857   90.536
LGA    G    67_A      G    67_A     0.275     0    0.018   0.018     0.383  100.000  100.000
LGA    K    68_A      K    68_A     0.315     0    0.018   1.297     6.454  100.000   71.905
LGA    F    69_A      F    69_A     0.682     0    0.024   0.145     0.864   90.476   90.476
LGA    A    70_A      A    70_A     0.627     0    0.026   0.025     0.652   90.476   90.476
LGA    V    71_A      V    71_A     0.346     0    0.013   0.035     0.409  100.000  100.000
LGA    D    72_A      D    72_A     0.346     0    0.016   0.042     0.463  100.000  100.000
LGA    E    73_A      E    73_A     0.500     0    0.023   0.061     0.626   97.619   93.651
LGA    E    74_A      E    74_A     0.592     0    0.024   1.281     4.647   90.476   72.222
LGA    N    75_A      N    75_A     0.413     0    0.031   0.093     0.500  100.000  100.000
LGA    K    76_A      K    76_A     0.339     0    0.044   0.114     0.637   97.619   98.942
LGA    I    77_A      I    77_A     0.546     0    0.041   0.073     0.776   90.476   90.476
LGA    G    78_A      G    78_A     0.690     0    0.067   0.067     0.690   90.476   90.476
LGA    Q    79_A      Q    79_A     0.490     0    0.028   0.890     3.670   95.238   78.413
LGA    Y    80_A      Y    80_A     0.772     0    0.051   0.065     1.119   88.214   87.460
LGA    G    81_A      G    81_A     0.794     0    0.086   0.086     1.087   88.214   88.214
LGA    R    82_A      R    82_A     0.633     0    0.021   1.033     4.963   95.238   72.814
LGA    L    83_A      L    83_A     0.450     0    0.015   0.103     0.538  100.000   98.810
LGA    T    84_A      T    84_A     0.486     0    0.032   0.033     0.557   97.619   94.558
LGA    F    85_A      F    85_A     0.388     0    0.031   0.136     0.729  100.000   96.537
LGA    N    86_A      N    86_A     0.537     0    0.009   1.096     3.180   95.238   85.536
LGA    K    87_A      K    87_A     0.354     0    0.018   0.117     1.121  100.000   93.757
LGA    V    88_A      V    88_A     0.223     0    0.023   0.046     0.277  100.000  100.000
LGA    I    89_A      I    89_A     0.299     0    0.034   0.056     0.609  100.000   98.810
LGA    R    90_A      R    90_A     0.165     0    0.015   1.204     4.792  100.000   82.121
LGA    P    91_A      P    91_A     0.122     0    0.027   0.077     0.474  100.000  100.000
LGA    C    92_A      C    92_A     0.356     0    0.027   0.057     0.450  100.000  100.000
LGA    M    93_A      M    93_A     0.516     0    0.027   0.922     3.165   97.619   88.988
LGA    K    94_A      K    94_A     0.460     0    0.041   0.073     0.605   97.619   98.942
LGA    K    95_A      K    95_A     0.240     0    0.089   0.591     1.553  100.000   91.746
LGA    T    96_A      T    96_A     0.830     0    0.016   0.034     1.291   90.476   87.891
LGA    I    97_A      I    97_A     0.925     0    0.042   0.367     2.190   88.214   86.131
LGA    Y    98_A      Y    98_A     1.173     0    0.061   0.119     1.341   81.429   81.429
LGA    E    99_A      E    99_A     1.280     0    0.635   0.936     3.868   73.214   63.122

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       50     200    200  100.00     401    401  100.00                97
SUMMARY(RMSD_GDC):     1.052          1.116                  1.389           47.420   44.967

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50   97    4.0     50    1.05    50.000    50.705     4.340

LGA_LOCAL      RMSD:   1.052  Number of atoms:   50  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.052  Number of assigned atoms:   50 
Std_ASGN_ATOMS RMSD:   1.052  Standard rmsd on all 50 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.160873 * X  +   0.022313 * Y  +   0.986723 * Z  +   1.457031
  Y_new =   0.861065 * X  +   0.491790 * Y  +   0.129265 * Z  +   5.798192
  Z_new =  -0.482376 * X  +   0.870428 * Y  +  -0.098328 * Z  +  49.555092 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.755497  0.503365  1.683285   [DEG:  100.5826   28.8407   96.4451 ]
ZXZ:  1.701059  1.669284 -0.506048   [DEG:   97.4635   95.6429  -28.9944 ]
 
# END of job
