
#######################################################
#                                                     #
#                        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 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   97 (  780),  selected   49 , 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:    49      52_A - 100_A       1.08     1.08
  LCS_AVERAGE:     50.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      52_A - 100_A       1.08     1.08
  LCS_AVERAGE:     50.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      52_A - 99_A        0.99     1.09
  LCS_AVERAGE:     48.90

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     G    52_A     G    52_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    53_A     E    53_A     48   49   49     25   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     W    54_A     W    54_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    55_A     E    55_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    56_A     I    56_A     48   49   49     27   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    57_A     I    57_A     48   49   49      9   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    58_A     D    58_A     48   49   49      8   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    59_A     I    59_A     48   49   49     15   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    60_A     G    60_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     P    61_A     P    61_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F    62_A     F    62_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    63_A     T    63_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    64_A     Q    64_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    65_A     N    65_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    66_A     L    66_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    67_A     G    67_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    68_A     K    68_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F    69_A     F    69_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    70_A     A    70_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    71_A     V    71_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    72_A     D    72_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    73_A     E    73_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    74_A     E    74_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    75_A     N    75_A     48   49   49     24   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    76_A     K    76_A     48   49   49      4   40   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    77_A     I    77_A     48   49   49      3   19   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    78_A     G    78_A     48   49   49      3    4    8   37   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    79_A     Q    79_A     48   49   49      3    9   13   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Y    80_A     Y    80_A     48   49   49      3    9   13   31   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    81_A     G    81_A     48   49   49     18   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    82_A     R    82_A     48   49   49      4   22   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    83_A     L    83_A     48   49   49     18   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    84_A     T    84_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F    85_A     F    85_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    86_A     N    86_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    87_A     K    87_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    88_A     V    88_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    89_A     I    89_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    90_A     R    90_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     P    91_A     P    91_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     C    92_A     C    92_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    93_A     M    93_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    94_A     K    94_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    95_A     K    95_A     48   49   49     24   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    96_A     T    96_A     48   49   49     20   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    97_A     I    97_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Y    98_A     Y    98_A     48   49   49     30   41   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    99_A     E    99_A     48   49   49      3   37   43   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N   100_A     N   100_A     20   49   49      0    3    3   11   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  49.98  (  48.90   50.52   50.52 )

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     30     41     43     46     47     49     49     49     49     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  30.93  42.27  44.33  47.42  48.45  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52  50.52
GDT RMS_LOCAL    0.34   0.52   0.59   0.81   0.90   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08
GDT RMS_ALL_AT   1.19   1.21   1.17   1.11   1.10   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08

# Checking swapping
#   possible swapping detected:  E    53_A      E    53_A
#   possible swapping detected:  D    58_A      D    58_A
#   possible swapping detected:  Y    80_A      Y    80_A
#   possible swapping detected:  F    85_A      F    85_A
#   possible swapping detected:  E    99_A      E    99_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    52_A      G    52_A     0.689     0    0.486   0.486     1.558   90.833   90.833
LGA    E    53_A      E    53_A     0.715     0    0.041   1.036     2.915   90.476   77.249
LGA    W    54_A      W    54_A     0.479     0    0.043   0.094     1.330  100.000   88.673
LGA    E    55_A      E    55_A     0.670     0    0.022   0.985     5.588   90.476   65.397
LGA    I    56_A      I    56_A     0.838     0    0.067   0.637     1.687   88.214   87.143
LGA    I    57_A      I    57_A     0.928     0    0.065   0.098     1.196   92.857   87.143
LGA    D    58_A      D    58_A     1.377     0    0.068   0.950     4.829   83.690   67.262
LGA    I    59_A      I    59_A     0.607     0    0.289   1.618     3.796   97.619   78.929
LGA    G    60_A      G    60_A     0.138     0    0.023   0.023     0.236  100.000  100.000
LGA    P    61_A      P    61_A     0.176     0    0.040   0.107     0.648  100.000   97.279
LGA    F    62_A      F    62_A     0.458     0    0.057   0.077     0.536   97.619   97.403
LGA    T    63_A      T    63_A     0.479     0    0.040   0.892     2.098  100.000   89.728
LGA    Q    64_A      Q    64_A     0.382     0    0.043   0.665     2.167  100.000   86.032
LGA    N    65_A      N    65_A     0.308     0    0.083   1.080     3.163  100.000   89.048
LGA    L    66_A      L    66_A     0.374     0    0.047   1.269     3.130  100.000   87.202
LGA    G    67_A      G    67_A     0.323     0    0.047   0.047     0.375  100.000  100.000
LGA    K    68_A      K    68_A     0.283     0    0.040   0.599     2.287  100.000   91.005
LGA    F    69_A      F    69_A     0.367     0    0.047   0.113     1.320  100.000   92.338
LGA    A    70_A      A    70_A     0.389     0    0.044   0.043     0.450  100.000  100.000
LGA    V    71_A      V    71_A     0.519     0    0.044   0.929     2.074   92.857   87.007
LGA    D    72_A      D    72_A     0.657     0    0.027   0.095     1.059   92.857   89.405
LGA    E    73_A      E    73_A     0.596     0    0.045   0.268     1.785   92.857   86.561
LGA    E    74_A      E    74_A     0.626     0    0.054   1.217     4.649   92.857   75.026
LGA    N    75_A      N    75_A     1.023     0    0.105   0.192     1.243   83.690   83.690
LGA    K    76_A      K    76_A     1.317     0    0.190   0.780     2.760   81.429   76.085
LGA    I    77_A      I    77_A     1.585     0    0.056   1.098     3.547   75.000   69.286
LGA    G    78_A      G    78_A     2.756     0    0.535   0.535     2.756   65.000   65.000
LGA    Q    79_A      Q    79_A     2.325     0    0.040   1.394     6.393   59.524   49.365
LGA    Y    80_A      Y    80_A     2.725     0    0.694   0.555     6.778   57.500   39.008
LGA    G    81_A      G    81_A     1.327     0    0.162   0.162     2.276   75.119   75.119
LGA    R    82_A      R    82_A     1.703     0    0.132   1.383     9.695   77.143   45.584
LGA    L    83_A      L    83_A     1.151     0    0.091   0.171     1.973   85.952   81.548
LGA    T    84_A      T    84_A     0.629     0    0.097   0.127     0.885   90.476   91.837
LGA    F    85_A      F    85_A     0.454     0    0.081   0.274     0.773   97.619   95.671
LGA    N    86_A      N    86_A     0.632     0    0.141   1.018     2.585   90.476   83.095
LGA    K    87_A      K    87_A     0.785     0    0.057   0.983     3.007   90.476   82.011
LGA    V    88_A      V    88_A     0.690     0    0.038   0.124     0.760   90.476   90.476
LGA    I    89_A      I    89_A     0.598     0    0.042   0.070     0.892   95.238   92.857
LGA    R    90_A      R    90_A     0.192     0    0.049   1.425     7.784  100.000   69.437
LGA    P    91_A      P    91_A     0.333     0    0.043   0.219     0.748  100.000   97.279
LGA    C    92_A      C    92_A     0.422     0    0.101   0.102     0.644   95.238   96.825
LGA    M    93_A      M    93_A     0.540     0    0.031   1.224     5.444   90.476   76.071
LGA    K    94_A      K    94_A     0.786     0    0.099   0.537     1.672   83.810   81.587
LGA    K    95_A      K    95_A     1.217     0    0.082   0.869     1.755   83.690   80.582
LGA    T    96_A      T    96_A     1.054     0    0.094   1.064     3.084   79.286   72.245
LGA    I    97_A      I    97_A     0.417     0    0.132   0.363     1.986   97.619   93.036
LGA    Y    98_A      Y    98_A     0.522     0    0.096   0.272     1.935   95.238   88.492
LGA    E    99_A      E    99_A     1.108     0    0.607   0.791     3.242   77.619   68.889
LGA    N   100_A      N   100_A     3.000     0    0.629   0.692     4.954   47.262   56.071

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     401    401  100.00                97
SUMMARY(RMSD_GDC):     1.078          1.131                  1.988           45.037   41.359

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50   97    4.0     49    1.08    47.680    49.050     4.160

LGA_LOCAL      RMSD:   1.078  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.078  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.078  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.386353 * X  +   0.913958 * Y  +  -0.124147 * Z  +  -9.800217
  Y_new =  -0.904537 * X  +  -0.349117 * Y  +   0.244806 * Z  +  61.354771
  Z_new =   0.180401 * X  +   0.206877 * Y  +   0.961591 * Z  +  10.136137 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.974468 -0.181394  0.211910   [DEG: -113.1287  -10.3931   12.1416 ]
ZXZ: -2.672263  0.278055  0.717139   [DEG: -153.1094   15.9314   41.0891 ]
 
# END of job
