
#######################################################
#                                                     #
#                        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   99 (  793),  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        0.52     0.52
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.52     0.52
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.52     0.52
  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     50   59   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     47   59   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     50   59   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     50   59   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     15   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     16   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     46   59   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     49   59   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      3   59   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      9   54   60   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     50   59   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     48   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     23   59   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     49   59   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    3   42   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     50     59     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  81.97  96.72  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    0.33   0.40   0.44   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52
GDT RMS_ALL_AT   0.53   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52

# Checking swapping
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  D    95_A      D    95_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     0.436     0    0.455   0.458     2.219   90.833   85.619
LGA    T    33_A      T    33_A     0.627     0    0.085   0.316     1.340   90.476   89.184
LGA    M    34_A      M    34_A     0.523     0    0.045   1.118     2.565   95.238   85.536
LGA    A    35_A      A    35_A     0.388     0    0.091   0.108     0.844   95.238   96.190
LGA    D    36_A      D    36_A     0.887     0    0.130   0.352     2.745   95.238   81.071
LGA    L    37_A      L    37_A     0.244     0    0.023   0.168     0.569  100.000   98.810
LGA    K    38_A      K    38_A     0.381     0    0.054   0.697     1.902   97.619   90.794
LGA    M    39_A      M    39_A     0.287     0    0.018   0.506     1.680  100.000   95.417
LGA    Q    40_A      Q    40_A     0.226     0    0.019   0.798     3.868  100.000   84.180
LGA    A    41_A      A    41_A     0.229     0    0.079   0.090     0.430  100.000  100.000
LGA    V    42_A      V    42_A     0.303     0    0.086   0.135     0.596   97.619   98.639
LGA    K    43_A      K    43_A     0.254     0    0.006   0.092     0.449  100.000  100.000
LGA    E    44_A      E    44_A     0.281     0    0.172   0.252     1.009   95.357   96.878
LGA    I    45_A      I    45_A     0.125     0    0.024   0.121     0.763  100.000   98.810
LGA    C    46_A      C    46_A     0.174     0    0.118   0.142     0.729   97.619   98.413
LGA    Y    47_A      Y    47_A     0.057     0    0.047   0.119     1.916  100.000   89.246
LGA    E    48_A      E    48_A     0.173     0    0.023   0.170     0.467  100.000  100.000
LGA    V    49_A      V    49_A     0.450     0    0.041   0.064     0.604  100.000   95.918
LGA    A    50_A      A    50_A     0.400     0    0.057   0.055     0.569   97.619   98.095
LGA    L    51_A      L    51_A     0.359     0    0.164   0.290     1.963   97.619   88.512
LGA    A    52_A      A    52_A     0.557     0    0.029   0.028     0.716   92.857   92.381
LGA    D    53_A      D    53_A     0.409     0    0.029   0.892     4.287   97.619   80.000
LGA    F    54_A      F    54_A     0.404     0    0.072   0.070     0.583   97.619   97.403
LGA    R    55_A      R    55_A     0.595     0    0.070   1.255     7.112   97.619   61.255
LGA    H    56_A      H    56_A     0.160     0    0.079   0.386     1.063   97.619   95.286
LGA    G    57_A      G    57_A     0.586     0    0.053   0.053     0.586   97.619   97.619
LGA    R    58_A      R    58_A     0.345     0    0.060   1.098     5.021  100.000   75.498
LGA    A    59_A      A    59_A     0.348     0    0.040   0.038     0.451  100.000  100.000
LGA    E    60_A      E    60_A     0.256     0    0.010   0.554     1.977  100.000   92.804
LGA    I    61_A      I    61_A     0.283     0    0.010   0.124     0.449  100.000  100.000
LGA    E    62_A      E    62_A     0.249     0    0.026   0.215     0.888  100.000   96.825
LGA    A    63_A      A    63_A     0.426     0    0.018   0.020     0.538  100.000   98.095
LGA    L    64_A      L    64_A     0.370     0    0.215   0.441     1.760   97.619   89.583
LGA    A    65_A      A    65_A     0.250     0    0.022   0.022     0.489  100.000  100.000
LGA    A    66_A      A    66_A     0.483     0    0.047   0.049     0.704   97.619   96.190
LGA    L    67_A      L    67_A     0.262     0    0.052   0.747     2.884  100.000   88.929
LGA    K    68_A      K    68_A     0.212     0    0.029   0.288     1.933  100.000   93.862
LGA    M    69_A      M    69_A     0.373     0    0.021   0.560     1.448  100.000   94.167
LGA    R    70_A      R    70_A     0.269     0    0.083   1.266     3.170   97.619   84.589
LGA    E    71_A      E    71_A     0.507     0    0.105   0.701     1.907   97.619   88.730
LGA    L    72_A      L    72_A     0.435     0    0.033   0.178     0.630  100.000   98.810
LGA    C    73_A      C    73_A     0.404     0    0.074   0.215     1.056  100.000   96.905
LGA    R    74_A      R    74_A     0.604     0    0.306   0.750     5.781   86.429   66.104
LGA    T    75_A      T    75_A     0.526     0    0.121   0.188     1.444   97.619   93.265
LGA    Y    76_A      Y    76_A     0.825     0    0.686   0.616     2.288   84.048   86.071
LGA    G    83_A      G    83_A     1.341     0    0.233   0.233     1.341   88.214   88.214
LGA    D    84_A      D    84_A     0.293     0    0.060   0.696     1.491   95.238   91.786
LGA    A    85_A      A    85_A     0.590     0    0.018   0.017     0.846   95.238   94.286
LGA    W    86_A      W    86_A     0.393     0    0.038   0.072     0.886   97.619   93.197
LGA    R    87_A      R    87_A     0.444     0    0.017   0.952     2.619   97.619   88.398
LGA    A    88_A      A    88_A     0.264     0    0.139   0.160     0.884   97.619   98.095
LGA    V    89_A      V    89_A     0.329     0    0.054   0.101     0.590   97.619   97.279
LGA    A    90_A      A    90_A     0.335     0    0.056   0.066     0.409  100.000  100.000
LGA    R    91_A      R    91_A     0.207     0    0.035   1.213     5.598  100.000   79.740
LGA    D    92_A      D    92_A     0.156     0    0.068   0.102     0.456  100.000  100.000
LGA    V    93_A      V    93_A     0.352     0    0.019   0.043     0.528  100.000   98.639
LGA    W    94_A      W    94_A     0.397     0    0.013   0.075     1.205  100.000   89.966
LGA    D    95_A      D    95_A     0.372     0    0.151   0.613     2.761   92.976   83.333
LGA    T    96_A      T    96_A     0.648     0    0.074   1.160     2.579   97.619   84.830
LGA    V    97_A      V    97_A     0.470     0    0.481   0.385     1.906   90.833   92.041
LGA    G    98_A      G    98_A     2.138     0    0.375   0.375     2.138   77.381   77.381

# 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):     0.516          0.537                  1.216           97.016   91.686

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    0.52    99.180    99.619     9.902

LGA_LOCAL      RMSD:   0.516  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.516  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.516  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.148170 * X  +  -0.872686 * Y  +  -0.465259 * Z  +  -0.245742
  Y_new =  -0.511472 * X  +  -0.335027 * Y  +   0.791298 * Z  +  24.098753
  Z_new =  -0.846429 * X  +   0.355214 * Y  +  -0.396714 * Z  + -12.674822 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.852771  1.009243  2.411330   [DEG: -106.1559   57.8253  138.1590 ]
ZXZ: -2.610067  1.978730 -1.173456   [DEG: -149.5458  113.3729  -67.2341 ]
 
# END of job
