
#######################################################
#                                                     #
#                        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   97 (  779),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     A    32_A     A    32_A     61   61   61     16   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     61   61   61     40   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     61   61   61     28   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     61   61   61     38   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     61   61   61     40   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     61   61   61     30   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     61   61   61      7   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     61   61   61     15   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     61   61   61     39   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     61   61   61     38   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     61   61   61     40   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     61   61   61     39   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     61   61   61     39   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     61   61   61      3   28   55   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     61   61   61     15   35   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     61   61   61     17   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     61   61   61     41   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     61   61   61     38   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     61   61   61     15   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     61   61   61     35   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     61   61   61      3   26   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
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     41     57     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  67.21  93.44  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.49   0.55   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61
GDT RMS_ALL_AT   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     0.811     0    0.491   0.502     1.671   85.952   83.333
LGA    T    33_A      T    33_A     0.344     0    0.093   0.359     1.081   97.619   93.333
LGA    M    34_A      M    34_A     0.253     0    0.065   0.193     1.129  100.000   95.298
LGA    A    35_A      A    35_A     0.587     0    0.097   0.107     0.961   92.857   92.381
LGA    D    36_A      D    36_A     1.011     0    0.125   0.263     2.993   92.976   78.929
LGA    L    37_A      L    37_A     0.085     0    0.047   0.119     0.316  100.000  100.000
LGA    K    38_A      K    38_A     0.407     0    0.077   0.681     1.801   97.619   90.688
LGA    M    39_A      M    39_A     0.446     0    0.038   0.827     1.723  100.000   92.024
LGA    Q    40_A      Q    40_A     0.295     0    0.022   0.170     0.602  100.000   97.884
LGA    A    41_A      A    41_A     0.173     0    0.061   0.069     0.409  100.000  100.000
LGA    V    42_A      V    42_A     0.385     0    0.103   0.182     0.665   97.619   98.639
LGA    K    43_A      K    43_A     0.409     0    0.039   0.139     1.573  100.000   91.746
LGA    E    44_A      E    44_A     0.326     0    0.152   0.289     0.867   97.619   97.884
LGA    I    45_A      I    45_A     0.079     0    0.033   0.098     0.700  100.000   98.810
LGA    C    46_A      C    46_A     0.122     0    0.113   0.144     0.704   97.619   98.413
LGA    Y    47_A      Y    47_A     0.172     0    0.026   0.254     1.107  100.000   94.484
LGA    E    48_A      E    48_A     0.390     0    0.023   0.899     2.500   97.619   84.233
LGA    V    49_A      V    49_A     0.507     0    0.052   0.075     0.662   97.619   94.558
LGA    A    50_A      A    50_A     0.287     0    0.154   0.157     0.890   97.619   98.095
LGA    L    51_A      L    51_A     0.480     0    0.104   0.302     2.365   95.238   84.167
LGA    A    52_A      A    52_A     0.676     0    0.091   0.085     0.915   90.476   90.476
LGA    D    53_A      D    53_A     0.599     0    0.089   0.162     1.459   90.476   87.083
LGA    F    54_A      F    54_A     0.418     0    0.088   0.128     0.818   95.238   96.537
LGA    R    55_A      R    55_A     0.966     0    0.156   1.487    10.312   92.857   53.074
LGA    H    56_A      H    56_A     0.210     0    0.092   0.322     1.049   90.595   92.524
LGA    G    57_A      G    57_A     1.207     0    0.071   0.071     1.207   88.214   88.214
LGA    R    58_A      R    58_A     0.878     0    0.030   1.132     5.582   92.857   66.147
LGA    A    59_A      A    59_A     0.695     0    0.056   0.051     0.817   90.476   90.476
LGA    E    60_A      E    60_A     0.511     0    0.019   0.407     1.521   95.238   90.688
LGA    I    61_A      I    61_A     0.099     0    0.019   0.063     0.359  100.000  100.000
LGA    E    62_A      E    62_A     0.518     0    0.044   0.158     1.078   95.238   91.587
LGA    A    63_A      A    63_A     0.638     0    0.022   0.020     0.750   90.476   90.476
LGA    L    64_A      L    64_A     0.423     0    0.212   0.432     1.692   92.976   88.393
LGA    A    65_A      A    65_A     0.131     0    0.031   0.029     0.387  100.000  100.000
LGA    A    66_A      A    66_A     0.487     0    0.051   0.052     0.752   97.619   96.190
LGA    L    67_A      L    67_A     0.191     0    0.017   0.730     2.533  100.000   91.131
LGA    K    68_A      K    68_A     0.304     0    0.033   0.497     2.170  100.000   90.952
LGA    M    69_A      M    69_A     0.421     0    0.049   0.549     1.082  100.000   94.167
LGA    R    70_A      R    70_A     0.260     0    0.061   1.253     3.992  100.000   76.926
LGA    E    71_A      E    71_A     0.544     0    0.110   0.673     1.929   95.238   90.635
LGA    L    72_A      L    72_A     0.484     0    0.025   0.155     0.723   97.619   97.619
LGA    C    73_A      C    73_A     0.427     0    0.090   0.263     0.937   95.238   95.238
LGA    R    74_A      R    74_A     0.620     0    0.238   0.782     5.846   86.071   65.108
LGA    T    75_A      T    75_A     0.287     0    0.109   0.293     1.186   97.619   94.626
LGA    Y    76_A      Y    76_A     0.559     0    0.685   0.637     2.642   84.524   87.738
LGA    G    83_A      G    83_A     1.990     0    0.503   0.503     3.623   65.476   65.476
LGA    D    84_A      D    84_A     1.183     0    0.101   0.218     1.255   81.429   84.821
LGA    A    85_A      A    85_A     0.757     0    0.025   0.025     1.018   95.238   92.476
LGA    W    86_A      W    86_A     0.206     0    0.037   0.121     1.070  100.000   94.626
LGA    R    87_A      R    87_A     0.477     0    0.152   1.129     2.458   97.619   85.108
LGA    A    88_A      A    88_A     0.349     0    0.199   0.220     1.103   92.976   92.476
LGA    V    89_A      V    89_A     0.357     0    0.079   0.118     0.583   97.619   95.918
LGA    A    90_A      A    90_A     0.258     0    0.051   0.059     0.366  100.000  100.000
LGA    R    91_A      R    91_A     0.298     0    0.040   1.028     3.358  100.000   81.732
LGA    D    92_A      D    92_A     0.378     0    0.044   0.233     1.237  100.000   94.167
LGA    V    93_A      V    93_A     0.220     0    0.032   0.073     0.476  100.000  100.000
LGA    W    94_A      W    94_A     0.389     0    0.016   1.420     7.928  100.000   54.660
LGA    D    95_A      D    95_A     0.682     0    0.227   0.431     2.844   90.476   78.750
LGA    T    96_A      T    96_A     0.985     0    0.059   1.101     2.663   90.476   80.748
LGA    V    97_A      V    97_A     0.814     0    0.470   0.436     2.396   84.048   86.803
LGA    G    98_A      G    98_A     1.267     0    0.653   0.653     3.547   69.762   69.762

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     0.607          0.717                  1.559           94.625   88.991

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   61    4.0     61    0.61    98.361    99.360     8.629

LGA_LOCAL      RMSD:   0.607  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.607  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.607  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.644006 * X  +   0.438687 * Y  +  -0.626746 * Z  + -40.437420
  Y_new =   0.408330 * X  +   0.495685 * Y  +   0.766527 * Z  +  -4.424344
  Z_new =   0.646934 * X  +  -0.749567 * Y  +   0.140095 * Z  +  18.839685 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.565079 -0.703556 -1.386027   [DEG:   32.3766  -40.3108  -79.4135 ]
ZXZ: -2.456185  1.430239  2.429556   [DEG: -140.7290   81.9467  139.2033 ]
 
# END of job
