
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   52 (   52),  selected   47 , name T0372TS464_4_2
# Molecule2: number of CA atoms  298 ( 2427),  selected   47 , name T0372.pdb
# PARAMETERS: T0372TS464_4_2.T0372.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       102 - 114         1.98    30.92
  LONGEST_CONTINUOUS_SEGMENT:    13       219 - 231         4.88    21.65
  LONGEST_CONTINUOUS_SEGMENT:    13       220 - 232         4.59    21.08
  LONGEST_CONTINUOUS_SEGMENT:    13       225 - 237         4.66    18.80
  LONGEST_CONTINUOUS_SEGMENT:    13       226 - 238         4.94    18.87
  LCS_AVERAGE:      3.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       102 - 114         1.98    30.92
  LCS_AVERAGE:      2.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       102 - 108         0.87    27.99
  LCS_AVERAGE:      1.40

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:  298
LCS_GDT     K       5     K       5      4    5    5     3    4    4    5    5    5    5    5    6    6    6   12   12   13   14   16   18   20   21   22 
LCS_GDT     D       6     D       6      4    5    5     3    4    4    5    5    5    5    5    6    6    6    8    9   10   10   15   18   19   21   22 
LCS_GDT     I       7     I       7      4    5    5     3    4    4    5    5    5    5    5    6    6    6   12   12   13   14   16   18   20   21   22 
LCS_GDT     T       8     T       8      4    5    5     3    4    4    5    5    5    5    5    6    6    6   10   10   10   10   13   13   16   16   22 
LCS_GDT     L       9     L       9      4    5    5     3    4    4    5    5    5    5    5    6    8    8   10   10   10   10   10   10   16   16   17 
LCS_GDT     A     102     A     102      7   13   13     4    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     103     D     103      7   13   13     4    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   14   15 
LCS_GDT     L     104     L     104      7   13   13     4    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   14   15 
LCS_GDT     E     105     E     105      7   13   13     4    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     106     A     106      7   13   13     4    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   14   15 
LCS_GDT     I     107     I     107      7   13   13     4    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     108     L     108      7   13   13     4    5    7    8    9   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     P     109     P     109      4   13   13     4    4    4    4   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     110     E     110      4   13   13     4    4    4    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     R     111     R     111      4   13   13     3    4    4   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     112     F     112      4   13   13     3    6    7   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     113     I     113      4   13   13     3    5    6   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     114     F     114      4   13   13     3    4    6   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     213     V     213      3    4   11     3    3    3    4    4    4    6    7    8    9    9   10   11   11   12   14   14   15   19   22 
LCS_GDT     N     214     N     214      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   11   11   11   14   14   15   16   17 
LCS_GDT     G     215     G     215      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   10   11   11   12   13   14   15   16 
LCS_GDT     K     216     K     216      3    4   11     3    3    3    4    4    5    6    7    8    9    9   10   11   11   11   14   14   15   16   16 
LCS_GDT     I     217     I     217      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   11   11   12   14   15   18   19   22 
LCS_GDT     V     218     V     218      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   10   11   11   14   14   18   18   22 
LCS_GDT     A     219     A     219      3    4   13     3    3    3    4    4    4    6    6    7    9    9   10   10   11   12   13   14   18   18   22 
LCS_GDT     F     220     F     220      3    4   13     0    3    3    4    4    4    6    6    7    9    9   12   12   13   14   15   15   18   19   22 
LCS_GDT     T     221     T     221      3    7   13     1    3    3    4    6    7   10   10   11   11   11   12   12   13   14   15   15   18   18   22 
LCS_GDT     F     222     F     222      3    7   13     0    3    4    5    7    8   10   10   11   11   11   12   12   13   14   15   15   18   19   22 
LCS_GDT     G     223     G     223      3    7   13     3    3    5    5    7    8   10   10   11   11   11   12   12   12   14   15   15   18   19   21 
LCS_GDT     M     224     M     224      4    7   13     3    3    5    5    7    8   10   10   11   11   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     P     225     P     225      4    7   13     3    3    5    5    7    8   10   10   11   11   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     I     226     I     226      5    7   13     4    5    5    6    7    8   10   10   11   11   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     N     227     N     227      5    7   13     4    5    5    6    7    8   10   10   11   11   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     H     228     H     228      5    7   13     3    5    5    6    7    8   10   10   11   11   11   12   12   13   14   16   18   20   21   22 
LCS_GDT     E     229     E     229      5    6   13     4    5    5    6    6    8   10   10   11   11   11   12   12   13   14   16   18   20   21   22 
LCS_GDT     T     230     T     230      5    6   13     4    5    5    6    6    8   10   10   11   11   11   12   12   14   14   16   18   20   21   22 
LCS_GDT     F     231     F     231      3    6   13     2    4    5    6    6    6    6   10   11   11   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     G     232     G     232      3    3   13     3    3    3    3    3    5    6    9    9   10   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     V     233     V     233      3    4   13     3    3    3    5    5    5    6    9    9   10   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     H     234     H     234      3    4   13     3    3    3    5    5    5    6    9    9   10   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     V     235     V     235      3    4   13     3    3    3    5    5    5    6    8    9   10   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     E     236     E     236      3    4   13     3    3    3    5    5    5    6    8    9   10   11   12   13   14   15   16   18   20   21   22 
LCS_GDT     K     237     K     237      3    5   13     3    3    4    4    5    5    6    7    8   10   10   12   13   14   15   16   18   20   21   22 
LCS_GDT     A     238     A     238      4    5   13     3    4    4    4    5    5    6    7    8    8   10   12   13   14   15   16   18   20   21   22 
LCS_GDT     D     239     D     239      4    5   10     3    4    4    4    5    5    6    7    8    8    9   10   11   11   15   16   18   20   21   22 
LCS_GDT     T     240     T     240      4    5   10     3    4    4    4    5    5    6    7    8    8   10   12   13   14   15   16   18   20   21   22 
LCS_GDT     S     241     S     241      4    5   10     3    4    4    4    5    5    6    7    8    8    9   10   11   14   15   16   18   20   21   22 
LCS_AVERAGE  LCS_A:   2.59  (   1.40    2.46    3.93 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
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_CA      4      6      7     10     10     12     13     13     13     13     13     13     13     14     15     16     18     20     21     22 
GDT PERCENT_CA   1.34   2.01   2.35   3.36   3.36   4.03   4.36   4.36   4.36   4.36   4.36   4.36   4.36   4.70   5.03   5.37   6.04   6.71   7.05   7.38
GDT RMS_LOCAL    0.15   0.48   0.71   1.38   1.38   1.77   1.98   1.98   1.98   1.98   1.98   1.98   1.98   5.18   5.38   5.63   5.96   6.47   6.62   6.89
GDT RMS_ALL_CA  28.30  29.38  29.90  31.67  31.67  31.52  30.92  30.92  30.92  30.92  30.92  30.92  30.92  22.27  22.15  20.71  20.84  20.48  20.63  20.97

#      Molecule1      Molecule2       DISTANCE
LGA    K       5      K       5         26.676
LGA    D       6      D       6         27.027
LGA    I       7      I       7         25.135
LGA    T       8      T       8         26.729
LGA    L       9      L       9         27.640
LGA    A     102      A     102          1.050
LGA    D     103      D     103          0.934
LGA    L     104      L     104          0.859
LGA    E     105      E     105          1.751
LGA    A     106      A     106          1.780
LGA    I     107      I     107          0.851
LGA    L     108      L     108          3.023
LGA    P     109      P     109          2.755
LGA    E     110      E     110          3.297
LGA    R     111      R     111          2.516
LGA    F     112      F     112          1.773
LGA    I     113      I     113          1.020
LGA    F     114      F     114          1.788
LGA    V     213      V     213         48.490
LGA    N     214      N     214         50.802
LGA    G     215      G     215         52.586
LGA    K     216      K     216         53.008
LGA    I     217      I     217         50.013
LGA    V     218      V     218         46.827
LGA    A     219      A     219         45.711
LGA    F     220      F     220         46.772
LGA    T     221      T     221         42.727
LGA    F     222      F     222         40.879
LGA    G     223      G     223         40.996
LGA    M     224      M     224         38.639
LGA    P     225      P     225         37.150
LGA    I     226      I     226         31.814
LGA    N     227      N     227         34.138
LGA    H     228      H     228         37.740
LGA    E     229      E     229         35.542
LGA    T     230      T     230         30.248
LGA    F     231      F     231         31.152
LGA    G     232      G     232         27.976
LGA    V     233      V     233         26.557
LGA    H     234      H     234         23.647
LGA    V     235      V     235         25.282
LGA    E     236      E     236         24.647
LGA    K     237      K     237         24.718
LGA    A     238      A     238         27.918
LGA    D     239      D     239         30.309
LGA    T     240      T     240         25.391
LGA    S     241      S     241         28.305

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   52  298    4.0     13    1.98     3.775     3.488     0.625

LGA_LOCAL      RMSD =  1.980  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 30.919  Number of atoms =   47 
Std_ALL_ATOMS  RMSD = 17.207  (standard rmsd on all 47 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.280263 * X  +  -0.334479 * Y  +  -0.899764 * Z  +  57.903385
  Y_new =   0.726166 * X  +  -0.539151 * Y  +   0.426614 * Z  +  -5.586888
  Z_new =  -0.627802 * X  +  -0.772942 * Y  +   0.091783 * Z  + 107.469902 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.452604    1.688988  [ DEG:   -83.2281     96.7719 ]
  Theta =   0.678726    2.462866  [ DEG:    38.8882    141.1118 ]
  Phi   =   1.202461   -1.939132  [ DEG:    68.8959   -111.1041 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0372TS464_4_2                                
REMARK     2: T0372.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_2.T0372.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   52  298   4.0   13   1.98   3.488    17.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  LYS     5      25.384  57.112 -11.061  1.00  0.00
ATOM      2  CA  ASP     6      25.409  53.676  -9.456  1.00  0.00
ATOM      3  CA  ILE     7      25.931  52.628  -5.867  1.00  0.00
ATOM      4  CA  THR     8      27.301  49.449  -4.307  1.00  0.00
ATOM      5  CA  LEU     9      26.817  48.973  -0.543  1.00  0.00
ATOM      6  CA  ALA   102      20.022  57.374   3.518  1.00  0.00
ATOM      7  CA  ASP   103      23.357  58.915   2.560  1.00  0.00
ATOM      8  CA  LEU   104      23.562  56.928  -0.700  1.00  0.00
ATOM      9  CA  GLU   105      20.114  58.263  -1.513  1.00  0.00
ATOM     10  CA  ALA   106      21.550  61.776  -1.817  1.00  0.00
ATOM     11  CA  ILE   107      23.449  60.990  -5.005  1.00  0.00
ATOM     12  CA  LEU   108      20.256  59.595  -6.549  1.00  0.00
ATOM     13  CA  PRO   109      21.804  56.516  -8.153  1.00  0.00
ATOM     14  CA  GLU   110      20.028  54.938 -11.115  1.00  0.00
ATOM     15  CA  ARG   111      20.855  51.601  -9.562  1.00  0.00
ATOM     16  CA  PHE   112      21.700  50.587  -6.025  1.00  0.00
ATOM     17  CA  ILE   113      23.151  47.180  -5.314  1.00  0.00
ATOM     18  CA  PHE   114      23.647  45.912  -1.772  1.00  0.00
ATOM     19  CA  VAL   213      11.988  42.349   2.578  1.00  0.00
ATOM     20  CA  ASN   214      13.931  45.358   3.683  1.00  0.00
ATOM     21  CA  GLY   215      15.854  45.445   0.445  1.00  0.00
ATOM     22  CA  LYS   216      12.467  45.362  -1.373  1.00  0.00
ATOM     23  CA  ILE   217      11.343  48.575   0.351  1.00  0.00
ATOM     24  CA  VAL   218      14.219  51.081   0.001  1.00  0.00
ATOM     25  CA  ALA   219      14.536  50.541  -3.763  1.00  0.00
ATOM     26  CA  PHE   220      10.596  50.592  -3.996  1.00  0.00
ATOM     27  CA  THR   221      11.411  53.915  -2.340  1.00  0.00
ATOM     28  CA  PHE   222      14.414  54.646  -4.435  1.00  0.00
ATOM     29  CA  GLY   223      12.740  53.415  -7.644  1.00  0.00
ATOM     30  CA  MET   224      15.916  51.526  -8.524  1.00  0.00
ATOM     31  CA  PRO   225      15.789  47.765  -8.724  1.00  0.00
ATOM     32  CA  ILE   226      18.487  45.197  -8.068  1.00  0.00
ATOM     33  CA  ASN   227      19.903  42.009  -9.549  1.00  0.00
ATOM     34  CA  HIS   228      19.812  38.699  -7.843  1.00  0.00
ATOM     35  CA  GLU   229      23.481  38.983  -7.402  1.00  0.00
ATOM     36  CA  THR   230      23.328  42.330  -5.729  1.00  0.00
ATOM     37  CA  PHE   231      20.608  41.051  -3.493  1.00  0.00
ATOM     38  CA  GLY   232      22.646  38.033  -2.424  1.00  0.00
ATOM     39  CA  VAL   233      25.793  39.953  -1.882  1.00  0.00
ATOM     40  CA  HIS   234      24.114  42.557   0.279  1.00  0.00
ATOM     41  CA  VAL   235      22.330  39.824   2.192  1.00  0.00
ATOM     42  CA  GLU   236      25.588  38.164   2.793  1.00  0.00
ATOM     43  CA  LYS   237      27.253  41.139   4.438  1.00  0.00
ATOM     44  CA  ALA   238      24.623  42.929   6.461  1.00  0.00
ATOM     45  CA  ASP   239      22.158  40.269   7.501  1.00  0.00
ATOM     46  CA  THR   240      23.750  39.404  10.820  1.00  0.00
ATOM     47  CA  SER   241      20.939  37.151  12.205  1.00  0.00
ATOM     48  CA  MET   300      20.199  35.342   8.926  1.00  0.00
ATOM     49  CA  ASP   301      16.485  36.186   8.437  1.00  0.00
ATOM     50  CA  MET   302      16.767  37.479   4.772  1.00  0.00
ATOM     51  CA  VAL   303      15.795  40.999   5.853  1.00  0.00
ATOM     52  CA  ARG   304      18.430  43.761   6.081  1.00  0.00
TER
END
