
#######################################################
#                                                     #
#                        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   61 (  468),  selected   61 , name one
# Molecule2: number of CA atoms  243 ( 1787),  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:    33     186_A - 218_A       4.99    25.22
  LCS_AVERAGE:     11.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16     204_A - 219_A       1.95    26.25
  LONGEST_CONTINUOUS_SEGMENT:    16     205_A - 220_A       1.82    25.66
  LONGEST_CONTINUOUS_SEGMENT:    16     231_A - 246_A       1.39    49.37
  LCS_AVERAGE:      5.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15     205_A - 219_A       0.92    26.34
  LONGEST_CONTINUOUS_SEGMENT:    15     232_A - 246_A       0.47    50.22
  LCS_AVERAGE:      4.68

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     D   186_A     D   186_A      3    3   33      3    3    4    5    8   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     A   187_A     A   187_A      3   12   33      3    3    4    5    9   13   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     S   188_A     S   188_A      3   12   33      3    3    4    7   11   14   14   15   17   21   25   26   29   32   33   36   39   39   39   40 
LCS_GDT     A   189_A     A   189_A      9   12   33      5    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     I   190_A     I   190_A      9   12   33      5    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     V   191_A     V   191_A      9   12   33      5    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     A   192_A     A   192_A      9   12   33      5    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     L   193_A     L   193_A      9   12   33      5    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     H   194_A     H   194_A      9   12   33      4    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     T   195_A     T   195_A      9   12   33      4    7    9   11   12   14   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     D   196_A     D   196_A      9   12   33      4    6    9   11   12   14   14   15   17   23   25   27   29   32   32   36   39   39   39   40 
LCS_GDT     V   197_A     V   197_A      9   12   33      4    5    9   11   12   14   14   15   17   20   22   27   29   32   32   34   39   39   39   39 
LCS_GDT     M   198_A     M   198_A      5   12   33      3    4    9   11   12   14   14   15   16   20   22   27   29   32   32   36   39   39   39   40 
LCS_GDT     R   199_A     R   199_A      7   12   33      5    7    7   11   12   14   14   15   16   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     P   200_A     P   200_A      7    9   33      5    7    7    7   10   13   14   15   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     L   201_A     L   201_A      7    9   33      5    7    7    7    8    8    9   11   14   17   19   27   29   32   33   36   39   39   39   40 
LCS_GDT     A   202_A     A   202_A      7    9   33      5    7    7   10   12   14   14   15   16   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     D   203_A     D   203_A      7    9   33      5    7    7    7    8   12   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     A   204_A     A   204_A      7   16   33      5    7    7    7    8   12   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     G   205_A     G   205_A     15   16   33      5    7    7   14   15   15   15   17   17   21   23   27   29   32   33   36   39   39   39   40 
LCS_GDT     P   206_A     P   206_A     15   16   33      3   13   14   14   15   15   15   17   17   20   22   25   29   30   32   36   39   39   39   40 
LCS_GDT     T   207_A     T   207_A     15   16   33      9   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     L   208_A     L   208_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     I   209_A     I   209_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     E   210_A     E   210_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     T   211_A     T   211_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     L   212_A     L   212_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     D   213_A     D   213_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     A   214_A     A   214_A     15   16   33     12   13   14   14   15   15   15   17   17   23   25   27   29   32   33   36   39   39   39   40 
LCS_GDT     Y   215_A     Y   215_A     15   16   33     12   13   14   14   15   15   15   17   17   21   25   26   29   32   33   36   39   39   39   40 
LCS_GDT     L   216_A     L   216_A     15   16   33     12   13   14   14   15   15   15   17   17   18   20   25   29   32   33   36   39   39   39   40 
LCS_GDT     D   217_A     D   217_A     15   16   33     12   13   14   14   15   15   15   17   17   18   20   25   29   32   33   36   39   39   39   40 
LCS_GDT     C   218_A     C   218_A     15   16   33     12   13   14   14   15   15   15   17   17   18   20   23   29   32   33   36   39   39   39   40 
LCS_GDT     G   219_A     G   219_A     15   16   24     12   13   14   14   15   15   15   17   17   18   20   21   22   25   30   35   39   39   39   40 
LCS_GDT     G   220_A     G   220_A      3   16   24      3    3    4    5    7   12   15   16   17   18   20   21   26   30   33   36   39   39   39   40 
LCS_GDT     A   221_A     A   221_A     10   10   24      5   10   10   10   10   10   11   15   17   18   20   21   22   30   33   36   39   39   39   40 
LCS_GDT     I   222_A     I   222_A     10   10   24      9   10   10   10   10   10   10   13   16   16   20   21   23   30   32   36   39   39   39   40 
LCS_GDT     E   223_A     E   223_A     10   10   24      9   10   10   10   10   10   10   11   14   17   21   25   27   30   33   36   39   39   39   40 
LCS_GDT     A   224_A     A   224_A     10   10   24      9   10   10   10   10   10   10   10   12   17   19   22   27   30   33   36   39   39   39   40 
LCS_GDT     C   225_A     C   225_A     10   10   24      9   10   10   10   10   10   10   10   12   14   14   15   19   20   21   25   31   34   38   40 
LCS_GDT     A   226_A     A   226_A     10   10   22      9   10   10   10   10   10   10   10   12   14   14   15   19   20   22   25   28   34   37   40 
LCS_GDT     R   227_A     R   227_A     10   10   22      9   10   10   10   10   10   13   15   16   17   18   19   20   20   21   25   28   34   37   40 
LCS_GDT     K   228_A     K   228_A     10   10   22      9   10   10   10   10   10   13   15   16   17   18   19   20   20   21   22   22   24   25   30 
LCS_GDT     L   229_A     L   229_A     10   10   22      9   10   10   10   10   10   10   10   12   15   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     F   230_A     F   230_A     10   10   22      9   10   10   10   10   10   10   10   12   15   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     V   231_A     V   231_A      3   16   22      3    3    5   11   12   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     H   232_A     H   232_A     15   16   22     10   15   15   15   15   15   15   16   16   16   16   18   20   20   21   22   22   24   24   24 
LCS_GDT     P   233_A     P   233_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     N   234_A     N   234_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     T   235_A     T   235_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     V   236_A     V   236_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     R   237_A     R   237_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     Y   238_A     Y   238_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     R   239_A     R   239_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     L   240_A     L   240_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     K   241_A     K   241_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     R   242_A     R   242_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     I   243_A     I   243_A     15   16   22      8   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     T   244_A     T   244_A     15   16   22      8   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     D   245_A     D   245_A     15   16   22      7   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_GDT     F   246_A     F   246_A     15   16   22     11   15   15   15   15   15   15   16   16   17   18   19   20   20   21   22   22   24   24   24 
LCS_AVERAGE  LCS_A:   7.27  (   4.68    5.55   11.60 )

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     12     15     15     15     15     15     15     17     17     23     25     27     29     32     33     36     39     39     39     40 
GDT PERCENT_AT   4.94   6.17   6.17   6.17   6.17   6.17   6.17   7.00   7.00   9.47  10.29  11.11  11.93  13.17  13.58  14.81  16.05  16.05  16.05  16.46
GDT RMS_LOCAL    0.27   0.47   0.47   0.47   0.47   0.47   0.47   2.24   2.24   3.97   4.13   4.36   4.53   4.88   5.22   5.48   5.79   5.79   5.79   6.41
GDT RMS_ALL_AT  26.56  50.22  50.22  50.22  50.22  50.22  50.22  26.04  26.04  25.23  25.15  25.62  25.72  25.23  23.51  23.73  23.75  23.75  23.75  22.83

# Checking swapping
#   possible swapping detected:  E   210_A      E   210_A
#   possible swapping detected:  Y   215_A      Y   215_A
#   possible swapping detected:  F   230_A      F   230_A
#   possible swapping detected:  F   246_A      F   246_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D   186_A      D   186_A    17.095     0    0.631   1.054    17.662    0.000    0.000
LGA    A   187_A      A   187_A    17.155     0    0.274   0.271    17.870    0.000    0.000
LGA    S   188_A      S   188_A    18.363     0    0.306   0.670    20.973    0.000    0.000
LGA    A   189_A      A   189_A    20.882     0    0.234   0.222    22.491    0.000    0.000
LGA    I   190_A      I   190_A    16.345     0    0.022   0.650    17.890    0.000    0.000
LGA    V   191_A      V   191_A    16.711     0    0.072   0.073    18.552    0.000    0.000
LGA    A   192_A      A   192_A    20.058     0    0.066   0.079    22.115    0.000    0.000
LGA    L   193_A      L   193_A    17.994     0    0.044   1.381    21.392    0.000    0.000
LGA    H   194_A      H   194_A    13.235     0    0.063   0.857    14.729    0.000    0.048
LGA    T   195_A      T   195_A    15.732     0    0.046   1.047    18.559    0.000    0.000
LGA    D   196_A      D   196_A    17.861     0    0.187   0.325    20.950    0.000    0.000
LGA    V   197_A      V   197_A    15.824     0    0.131   0.176    17.220    0.000    0.000
LGA    M   198_A      M   198_A    14.122     0    0.606   1.125    14.821    0.000    0.000
LGA    R   199_A      R   199_A    14.010     0    0.578   1.443    20.267    0.000    0.000
LGA    P   200_A      P   200_A    13.871     0    0.022   0.269    18.167    0.000    0.000
LGA    L   201_A      L   201_A    13.243     0    0.111   1.381    18.248    0.357    0.179
LGA    A   202_A      A   202_A     8.771     0    0.063   0.061    10.393   13.929   11.238
LGA    D   203_A      D   203_A     4.338     0    0.023   1.019     6.303   31.786   24.464
LGA    A   204_A      A   204_A     5.172     0    0.111   0.131     7.642   43.571   36.286
LGA    G   205_A      G   205_A     2.753     0    0.713   0.713     2.753   62.857   62.857
LGA    P   206_A      P   206_A     3.085     0    0.066   0.182     3.828   55.357   54.218
LGA    T   207_A      T   207_A     2.090     0    0.087   1.155     3.895   68.810   61.905
LGA    L   208_A      L   208_A     1.982     0    0.061   0.129     2.781   70.833   66.845
LGA    I   209_A      I   209_A     1.534     0    0.070   0.071     1.822   77.143   77.143
LGA    E   210_A      E   210_A     0.901     0    0.025   0.750     3.555   88.214   73.968
LGA    T   211_A      T   211_A     1.249     0    0.034   0.133     2.038   83.690   77.891
LGA    L   212_A      L   212_A     1.251     0    0.023   1.415     2.680   83.690   76.548
LGA    D   213_A      D   213_A     0.741     0    0.055   0.114     0.968   90.476   90.476
LGA    A   214_A      A   214_A     0.677     0    0.049   0.061     1.016   90.595   90.571
LGA    Y   215_A      Y   215_A     0.543     0    0.065   0.088     1.588   92.857   85.317
LGA    L   216_A      L   216_A     1.177     0    0.058   0.071     1.958   81.548   78.274
LGA    D   217_A      D   217_A     1.334     0    0.107   0.256     1.864   81.429   78.214
LGA    C   218_A      C   218_A     1.070     0    0.264   0.362     1.595   79.286   81.508
LGA    G   219_A      G   219_A     1.487     0    0.336   0.336     4.010   62.500   62.500
LGA    G   220_A      G   220_A     7.769     0    0.266   0.266    10.891   10.357   10.357
LGA    A   221_A      A   221_A     8.608     0    0.594   0.558     9.567    2.976    4.381
LGA    I   222_A      I   222_A    10.248     0    0.021   0.591    13.195    0.357    0.417
LGA    E   223_A      E   223_A    14.146     0    0.024   0.788    20.023    0.000    0.000
LGA    A   224_A      A   224_A    13.399     0    0.063   0.072    15.583    0.000    0.000
LGA    C   225_A      C   225_A    14.380     0    0.088   0.316    18.342    0.000    0.000
LGA    A   226_A      A   226_A    18.899     0    0.043   0.043    22.567    0.000    0.000
LGA    R   227_A      R   227_A    21.576     0    0.070   0.946    24.201    0.000    0.000
LGA    K   228_A      K   228_A    20.788     0    0.092   0.313    24.286    0.000    0.000
LGA    L   229_A      L   229_A    24.738     0    0.121   1.021    28.800    0.000    0.000
LGA    F   230_A      F   230_A    29.023     0    0.478   1.330    33.237    0.000    0.000
LGA    V   231_A      V   231_A    32.051     0    0.608   1.441    33.953    0.000    0.000
LGA    H   232_A      H   232_A    32.397     0    0.594   1.121    34.168    0.000    0.000
LGA    P   233_A      P   233_A    31.342     0    0.070   0.114    34.328    0.000    0.000
LGA    N   234_A      N   234_A    36.018     0    0.103   0.757    39.610    0.000    0.000
LGA    T   235_A      T   235_A    39.422     0    0.031   0.981    41.163    0.000    0.000
LGA    V   236_A      V   236_A    37.939     0    0.037   0.059    40.728    0.000    0.000
LGA    R   237_A      R   237_A    39.613     0    0.024   1.063    43.261    0.000    0.000
LGA    Y   238_A      Y   238_A    44.697     0    0.045   1.234    47.666    0.000    0.000
LGA    R   239_A      R   239_A    46.080     0    0.043   0.154    48.263    0.000    0.000
LGA    L   240_A      L   240_A    45.508     0    0.104   0.170    48.652    0.000    0.000
LGA    K   241_A      K   241_A    49.013     0    0.049   0.594    53.127    0.000    0.000
LGA    R   242_A      R   242_A    52.787     0    0.035   1.605    55.282    0.000    0.000
LGA    I   243_A      I   243_A    52.660     0    0.052   0.633    55.851    0.000    0.000
LGA    T   244_A      T   244_A    54.624     0    0.053   0.191    58.464    0.000    0.000
LGA    D   245_A      D   245_A    58.933     0    0.198   0.175    61.521    0.000    0.000
LGA    F   246_A      F   246_A    61.113     0    0.652   1.293    65.098    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     468    468  100.00               243
SUMMARY(RMSD_GDC):    18.341         18.701                 19.266            5.237    4.961

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61  243    4.0     17    2.24     8.539     7.516     0.727

LGA_LOCAL      RMSD:   2.237  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  26.036  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:  18.341  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.200220 * X  +   0.217126 * Y  +  -0.955389 * Z  +  23.390369
  Y_new =   0.526461 * X  +  -0.798551 * Y  +  -0.291812 * Z  +  42.039024
  Z_new =  -0.826287 * X  +  -0.561402 * Y  +   0.045577 * Z  + -39.247631 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.934216  0.972484 -1.489789   [DEG:  110.8224   55.7192  -85.3586 ]
ZXZ: -1.274358  1.525203 -2.167581   [DEG:  -73.0153   87.3877 -124.1932 ]
 
# END of job
