
#######################################################
#                                                     #
#                        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   57 (  456),  selected   57 , name one
# Molecule2: number of CA atoms  213 ( 1696),  selected   57 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    55     183_A - 237_A       4.84     6.05
  LCS_AVERAGE:     25.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48     190_A - 237_A       1.68     7.73
  LCS_AVERAGE:     20.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46     192_A - 237_A       0.97     8.04
  LCS_AVERAGE:     18.29

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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     L   181_B     L   181_A     10   14   22      9   10   11   11   12   13   14   15   16   17   18   19   20   23   26   27   30   31   33   34 
LCS_GDT     Q   182_B     Q   182_A     10   14   22      9   10   11   11   12   13   14   15   16   17   18   19   20   26   26   27   30   31   34   41 
LCS_GDT     Q   183_B     Q   183_A     10   14   55      9   10   11   11   12   13   14   15   16   17   18   20   24   30   33   38   46   50   54   55 
LCS_GDT     Q   184_B     Q   184_A     10   14   55      9   10   11   11   12   13   14   15   16   17   18   24   28   32   37   45   51   53   54   55 
LCS_GDT     L   185_B     L   185_A     10   14   55      9   10   11   11   12   13   14   15   16   17   18   21   28   32   36   45   51   53   54   55 
LCS_GDT     Q   186_B     Q   186_A     10   14   55      9   10   11   11   12   13   14   15   16   22   27   39   44   48   51   52   52   53   54   55 
LCS_GDT     D   187_B     D   187_A     10   14   55      9   10   11   11   12   19   21   27   38   43   46   49   51   51   51   52   52   53   54   55 
LCS_GDT     I   188_B     I   188_A     10   14   55      9   10   11   11   12   13   14   16   26   35   44   48   51   51   51   52   52   53   54   55 
LCS_GDT     K   189_B     K   189_A     10   14   55      9   10   11   11   12   19   24   34   43   47   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     E   190_B     E   190_A     10   48   55      9   10   11   11   12   19   26   42   45   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     Q   191_B     Q   191_A      4   48   55      3    3    4    7   29   45   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     T   192_B     T   192_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     M   193_B     M   193_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   194_B     C   194_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     P   195_B     P   195_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     V   196_B     V   196_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   197_B     C   197_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     L   198_B     L   198_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     D   199_B     D   199_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     R   200_B     R   200_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     L   201_B     L   201_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     K   202_B     K   202_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     N   203_B     N   203_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     M   204_B     M   204_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     I   205_B     I   205_A     46   48   55      5   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     F   206_B     F   206_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     L   207_B     L   207_A     46   48   55      6   32   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   208_B     C   208_A     46   48   55      3   34   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     G   209_B     G   209_A     46   48   55     17   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     H   210_B     H   210_A     46   48   55     17   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     G   211_B     G   211_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     T   212_B     T   212_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   213_B     C   213_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     Q   214_B     Q   214_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     L   215_B     L   215_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   216_B     C   216_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     G   217_B     G   217_A     46   48   55     18   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     D   218_B     D   218_A     46   48   55      7   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     R   219_B     R   219_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     M   220_B     M   220_A     46   48   55     13   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     S   221_B     S   221_A     46   48   55     12   31   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     E   222_B     E   222_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   223_B     C   223_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     P   224_B     P   224_A     46   48   55     13   32   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     I   225_B     I   225_A     46   48   55     13   32   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     C   226_B     C   226_A     46   48   55     13   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     R   227_B     R   227_A     46   48   55     12   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     K   228_B     K   228_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     A   229_B     A   229_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     I   230_B     I   230_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     E   231_B     E   231_A     46   48   55      5   23   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     R   232_B     R   232_A     46   48   55     12   23   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     R   233_B     R   233_A     46   48   55     19   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     I   234_B     I   234_A     46   48   55     15   35   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     L   235_B     L   235_A     46   48   55     19   33   43   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     L   236_B     L   236_A     46   48   55      3   11   34   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_GDT     Y   237_B     Y   237_A     46   48   55      0   11   34   46   46   46   47   47   47   48   48   49   51   51   51   52   52   53   54   55 
LCS_AVERAGE  LCS_A:  21.19  (  18.29   20.01   25.28 )

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     19     35     43     46     46     46     47     47     47     48     48     49     51     51     51     52     52     53     54     55 
GDT PERCENT_AT   8.92  16.43  20.19  21.60  21.60  21.60  22.07  22.07  22.07  22.54  22.54  23.00  23.94  23.94  23.94  24.41  24.41  24.88  25.35  25.82
GDT RMS_LOCAL    0.26   0.69   0.83   0.97   0.97   0.97   1.18   1.18   1.18   1.68   1.68   2.07   2.85   2.85   2.85   3.39   3.39   4.33   4.39   4.84
GDT RMS_ALL_AT   8.48   8.17   8.06   8.04   8.04   8.04   8.00   8.00   8.00   7.73   7.73   7.50   6.99   6.99   6.99   6.69   6.69   6.19   6.23   6.05

# Checking swapping
#   possible swapping detected:  E   222_B      E   222_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L   181_B      L   181_A    28.673     0    0.106   1.357    30.917    0.000    0.000
LGA    Q   182_B      Q   182_A    26.446     0    0.054   0.268    32.262    0.000    0.000
LGA    Q   183_B      Q   183_A    23.378     0    0.037   1.076    25.040    0.000    0.000
LGA    Q   184_B      Q   184_A    20.471     0    0.018   0.647    25.747    0.000    0.000
LGA    L   185_B      L   185_A    18.727     0    0.034   0.119    23.685    0.000    0.000
LGA    Q   186_B      Q   186_A    16.993     0    0.059   0.493    23.043    0.000    0.000
LGA    D   187_B      D   187_A    13.110     0    0.148   1.228    15.080    0.357    0.179
LGA    I   188_B      I   188_A    10.988     0    0.102   0.227    15.750    1.310    0.655
LGA    K   189_B      K   189_A     9.472     0    0.177   0.973    14.084    4.881    2.169
LGA    E   190_B      E   190_A     8.778     0    0.603   0.780    13.570   10.000    4.444
LGA    Q   191_B      Q   191_A     4.520     0    0.232   0.829     6.424   37.976   29.577
LGA    T   192_B      T   192_A     0.818     0    0.625   1.020     5.086   88.214   66.803
LGA    M   193_B      M   193_A     0.529     0    0.032   0.662     3.252   90.476   83.214
LGA    C   194_B      C   194_A     0.530     0    0.072   0.117     1.155   90.595   90.556
LGA    P   195_B      P   195_A     0.890     0    0.022   0.083     1.070   88.214   90.544
LGA    V   196_B      V   196_A     0.955     0    0.025   0.048     1.227   88.214   87.891
LGA    C   197_B      C   197_A     0.861     0    0.020   0.074     1.001   88.214   88.968
LGA    L   198_B      L   198_A     0.901     0    0.075   0.653     1.964   88.214   86.012
LGA    D   199_B      D   199_A     0.493     0    0.179   0.354     1.168   90.595   89.405
LGA    R   200_B      R   200_A     0.394     0    0.089   1.334     6.580   97.619   73.550
LGA    L   201_B      L   201_A     0.615     0    0.057   0.222     0.757   90.476   92.857
LGA    K   202_B      K   202_A     0.842     0    0.119   0.601     2.054   88.214   80.741
LGA    N   203_B      N   203_A     0.881     0    0.027   1.202     4.713   90.476   74.762
LGA    M   204_B      M   204_A     1.037     0    0.083   0.226     1.893   79.286   79.345
LGA    I   205_B      I   205_A     0.846     0    0.016   1.072     5.382   95.238   72.738
LGA    F   206_B      F   206_A     0.764     0    0.647   0.764     3.740   76.667   84.675
LGA    L   207_B      L   207_A     1.200     0    0.051   0.157     2.335   81.429   75.119
LGA    C   208_B      C   208_A     1.155     0    0.096   0.739     4.082   85.952   77.063
LGA    G   209_B      G   209_A     0.167     0    0.083   0.083     0.632   95.238   95.238
LGA    H   210_B      H   210_A     0.185     0    0.028   1.148     3.058   97.619   84.238
LGA    G   211_B      G   211_A     0.609     0    0.094   0.094     0.609   97.619   97.619
LGA    T   212_B      T   212_A     0.228     0    0.025   0.141     0.423  100.000  100.000
LGA    C   213_B      C   213_A     0.408     0    0.021   0.089     0.677   95.238   93.651
LGA    Q   214_B      Q   214_A     0.819     0    0.048   1.237     3.772   90.476   78.571
LGA    L   215_B      L   215_A     0.857     0    0.129   1.302     3.286   90.476   78.036
LGA    C   216_B      C   216_A     0.837     0    0.149   0.210     0.941   92.857   92.063
LGA    G   217_B      G   217_A     0.544     0    0.018   0.018     0.781   95.238   95.238
LGA    D   218_B      D   218_A     1.021     0    0.047   0.125     1.794   85.952   82.619
LGA    R   219_B      R   219_A     0.824     0    0.121   1.143     3.082   90.476   81.212
LGA    M   220_B      M   220_A     0.861     0    0.127   0.734     1.830   88.214   87.143
LGA    S   221_B      S   221_A     1.179     0    0.138   0.177     1.913   88.214   83.095
LGA    E   222_B      E   222_A     0.591     0    0.017   0.830     2.723   90.476   80.000
LGA    C   223_B      C   223_A     0.552     0    0.016   0.067     0.857   92.857   92.063
LGA    P   224_B      P   224_A     1.222     0    0.134   0.332     1.945   81.548   82.857
LGA    I   225_B      I   225_A     1.346     0    0.028   0.628     2.453   81.429   76.131
LGA    C   226_B      C   226_A     1.170     0    0.019   0.175     1.170   81.429   82.937
LGA    R   227_B      R   227_A     1.123     0    0.090   1.349     3.096   83.690   74.069
LGA    K   228_B      K   228_A     0.454     0    0.091   1.167     6.847   97.619   69.418
LGA    A   229_B      A   229_A     0.587     0    0.068   0.087     0.922   92.857   92.381
LGA    I   230_B      I   230_A     0.567     0    0.076   0.149     1.280   85.952   89.464
LGA    E   231_B      E   231_A     1.813     0    0.158   0.860     6.747   77.143   54.603
LGA    R   232_B      R   232_A     1.656     0    0.062   0.205     3.077   77.143   65.238
LGA    R   233_B      R   233_A     0.349     0    0.134   1.475     8.470   97.619   61.558
LGA    I   234_B      I   234_A     0.411     0    0.112   1.128     3.207  100.000   81.905
LGA    L   235_B      L   235_A     1.223     0    0.044   0.424     3.773   79.405   69.464
LGA    L   236_B      L   236_A     2.381     0    0.617   0.649     5.308   53.452   60.179
LGA    Y   237_B      Y   237_A     2.263     0    0.051   1.151    11.548   63.095   33.333

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     456    456  100.00               213
SUMMARY(RMSD_GDC):     5.896          5.699                  6.665           19.230   17.585

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57  213    4.0     47    1.18    21.127    21.207     3.676

LGA_LOCAL      RMSD:   1.179  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.004  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:   5.896  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.980256 * X  +  -0.179008 * Y  +   0.083993 * Z  +   2.461929
  Y_new =  -0.133015 * X  +  -0.282672 * Y  +   0.949949 * Z  + -48.742310
  Z_new =  -0.146306 * X  +  -0.942366 * Y  +  -0.300902 * Z  + 106.204567 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.134871  0.146833 -1.879868   [DEG:   -7.7275    8.4129 -107.7085 ]
ZXZ:  3.053404  1.876434 -2.987568   [DEG:  174.9472  107.5118 -171.1751 ]
 
# END of job
