
#######################################################
#                                                     #
#                        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 (  415),  selected   49 , name one
# Molecule2: number of CA atoms   72 (  603),  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      33_A - 81_A        0.76     0.76
  LCS_AVERAGE:     68.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.76     0.76
  LCS_AVERAGE:     68.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.76     0.76
  LCS_AVERAGE:     68.06

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     Q    33_A     Q    33_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    34_A     L    34_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    35_A     L    35_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    36_A     S    36_A     49   49   49     23   40   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_A     G    37_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    38_A     I    38_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    39_A     V    39_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    40_A     Q    40_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    41_A     Q    41_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    42_A     Q    42_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    43_A     N    43_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    44_A     N    44_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    45_A     L    45_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_A     L    46_A     49   49   49     23   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    47_A     R    47_A     49   49   49     25   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    48_A     A    48_A     49   49   49     26   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    49_A     I    49_A     49   49   49     26   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    50_A     E    50_A     49   49   49     27   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    51_A     A    51_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    52_A     Q    52_A     49   49   49     29   40   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    53_A     Q    53_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    54_A     H    54_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    55_A     L    55_A     49   49   49     29   40   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    56_A     L    56_A     49   49   49     29   40   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    57_A     Q    57_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    58_A     L    58_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    59_A     T    59_A     49   49   49     29   40   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    60_A     V    60_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     W    61_A     W    61_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    62_A     G    62_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    63_A     I    63_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    64_A     K    64_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    65_A     Q    65_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    66_A     L    66_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    67_A     Q    67_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    68_A     A    68_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    69_A     R    69_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    70_A     I    70_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    71_A     L    71_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    72_A     A    72_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    73_A     V    73_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    74_A     E    74_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    75_A     R    75_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Y    76_A     Y    76_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    77_A     L    77_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    78_A     R    78_A     49   49   49     29   41   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    79_A     D    79_A     49   49   49     29   38   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    80_A     Q    80_A     49   49   49     29   38   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    81_A     Q    81_A     49   49   49     10   16   41   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  68.06  (  68.06   68.06   68.06 )

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     41     48     49     49     49     49     49     49     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  40.28  56.94  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06
GDT RMS_LOCAL    0.26   0.60   0.72   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76
GDT RMS_ALL_AT   1.67   0.77   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76   0.76

# Checking swapping
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    33_A      Q    33_A     0.865     0    0.084   0.389     2.098   88.214   81.693
LGA    L    34_A      L    34_A     0.556     0    0.044   0.435     2.128   90.476   86.131
LGA    L    35_A      L    35_A     0.891     0    0.006   0.479     1.761   88.214   83.750
LGA    S    36_A      S    36_A     1.263     0    0.049   0.635     3.034   81.429   76.190
LGA    G    37_A      G    37_A     0.878     0    0.031   0.031     0.991   90.476   90.476
LGA    I    38_A      I    38_A     0.679     0    0.025   0.048     0.783   90.476   90.476
LGA    V    39_A      V    39_A     1.050     0    0.017   0.061     1.232   83.690   82.721
LGA    Q    40_A      Q    40_A     1.107     0    0.017   0.772     2.102   83.690   79.630
LGA    Q    41_A      Q    41_A     0.478     0    0.035   0.839     3.654   97.619   85.714
LGA    Q    42_A      Q    42_A     0.592     0    0.061   0.573     2.097   92.857   88.677
LGA    N    43_A      N    43_A     0.598     0    0.018   0.982     3.356   95.238   86.667
LGA    N    44_A      N    44_A     0.131     0    0.022   0.076     0.643  100.000   97.619
LGA    L    45_A      L    45_A     0.325     0    0.016   0.201     0.759   97.619   96.429
LGA    L    46_A      L    46_A     0.550     0    0.025   0.637     2.899   95.238   87.560
LGA    R    47_A      R    47_A     0.156     0    0.026   0.434     2.339  100.000   93.377
LGA    A    48_A      A    48_A     0.518     0    0.023   0.024     0.659   92.857   92.381
LGA    I    49_A      I    49_A     0.671     0    0.033   0.102     0.947   90.476   90.476
LGA    E    50_A      E    50_A     0.408     0    0.051   0.752     3.731   95.238   81.693
LGA    A    51_A      A    51_A     0.631     0    0.022   0.021     0.842   92.857   92.381
LGA    Q    52_A      Q    52_A     1.167     0    0.031   0.081     1.985   83.690   79.577
LGA    Q    53_A      Q    53_A     0.950     0    0.026   0.187     1.608   88.214   85.503
LGA    H    54_A      H    54_A     0.661     0    0.023   1.215     5.138   90.476   65.619
LGA    L    55_A      L    55_A     1.263     0    0.040   0.913     3.496   81.429   71.429
LGA    L    56_A      L    56_A     1.321     0    0.038   1.372     3.513   81.429   74.524
LGA    Q    57_A      Q    57_A     0.635     0    0.025   1.202     3.640   95.238   83.386
LGA    L    58_A      L    58_A     0.644     0    0.031   0.175     1.307   90.476   88.214
LGA    T    59_A      T    59_A     1.138     0    0.047   0.073     1.595   88.214   84.082
LGA    V    60_A      V    60_A     0.847     0    0.012   0.064     1.073   90.476   89.184
LGA    W    61_A      W    61_A     0.110     0    0.065   1.281     9.069  100.000   52.075
LGA    G    62_A      G    62_A     0.682     0    0.030   0.030     0.682   90.476   90.476
LGA    I    63_A      I    63_A     0.785     0    0.015   0.092     1.258   90.476   88.214
LGA    K    64_A      K    64_A     0.434     0    0.054   1.172     6.235   97.619   74.286
LGA    Q    65_A      Q    65_A     0.232     0    0.034   0.643     1.500  100.000   91.693
LGA    L    66_A      L    66_A     0.461     0    0.028   0.272     1.695  100.000   91.905
LGA    Q    67_A      Q    67_A     0.456     0    0.023   0.788     4.350  100.000   80.476
LGA    A    68_A      A    68_A     0.268     0    0.025   0.030     0.372  100.000  100.000
LGA    R    69_A      R    69_A     0.235     0    0.019   0.885     3.780  100.000   89.048
LGA    I    70_A      I    70_A     0.456     0    0.048   1.384     3.898  100.000   83.929
LGA    L    71_A      L    71_A     0.517     0    0.017   0.053     0.678   95.238   92.857
LGA    A    72_A      A    72_A     0.296     0    0.037   0.046     0.356  100.000  100.000
LGA    V    73_A      V    73_A     0.151     0    0.025   0.065     0.306  100.000  100.000
LGA    E    74_A      E    74_A     0.489     0    0.021   0.187     1.306   95.238   91.587
LGA    R    75_A      R    75_A     0.678     0    0.045   0.258     1.938   90.476   87.229
LGA    Y    76_A      Y    76_A     0.553     0    0.014   0.061     0.914   90.476   91.270
LGA    L    77_A      L    77_A     0.542     0    0.015   0.067     0.736   90.476   95.238
LGA    R    78_A      R    78_A     0.815     0    0.028   1.264     7.663   90.476   60.130
LGA    D    79_A      D    79_A     1.056     0    0.065   0.059     1.493   83.690   85.952
LGA    Q    80_A      Q    80_A     1.118     0    0.051   0.282     1.894   81.429   80.476
LGA    Q    81_A      Q    81_A     1.694     0    0.320   0.827     2.147   77.143   79.683

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     404    404  100.00                72
SUMMARY(RMSD_GDC):     0.759          0.735                  1.662           62.632   58.223

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50   72    4.0     49    0.76    65.278    67.075     5.705

LGA_LOCAL      RMSD:   0.759  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.759  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   0.759  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.865737 * X  +   0.208393 * Y  +  -0.455052 * Z  +   0.120727
  Y_new =  -0.180344 * X  +  -0.978007 * Y  +  -0.104777 * Z  +   5.217151
  Z_new =  -0.466879 * X  +  -0.008644 * Y  +   0.884279 * Z  +  52.524395 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.936217  0.485758 -0.009775   [DEG: -168.2329   27.8319   -0.5600 ]
ZXZ: -1.344487  0.485848 -1.589308   [DEG:  -77.0334   27.8371  -91.0606 ]
 
# END of job
