
#######################################################
#                                                     #
#                        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   55 (   55),  selected   55 , name T0356TS464_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   55 , name T0356_D2.pdb
# PARAMETERS: T0356TS464_4-D2.T0356_D2.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:    31       233 - 280         4.74    19.48
  LCS_AVERAGE:     12.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       237 - 249         1.97    30.17
  LCS_AVERAGE:      3.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       240 - 249         0.66    29.57
  LCS_AVERAGE:      2.78

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:  192
LCS_GDT     T     122     T     122      3    3   13     0    3    3    3    3    3    4    8    9   10   11   12   14   14   14   15   15   16   16   16 
LCS_GDT     K     123     K     123      3    3   13     3    3    3    3    4    4    7    8    9   10   12   12   14   14   14   15   15   16   16   16 
LCS_GDT     R     124     R     124      3    3   13     3    3    3    3    4    6    7    8   10   11   12   12   14   14   14   15   15   16   16   16 
LCS_GDT     L     125     L     125      4    4   13     3    3    5    5    5    6    7    8   10   11   12   12   14   14   14   15   15   16   16   16 
LCS_GDT     R     126     R     126      4    4   13     3    3    5    5    5    5    6    7   10   11   12   12   14   14   14   15   15   16   16   16 
LCS_GDT     G     127     G     127      4    5   13     3    3    5    5    5    5    7    8   10   11   12   12   14   14   14   15   19   19   23   24 
LCS_GDT     A     128     A     128      4    5   13     4    4    5    5    5    6    7    8   10   11   12   12   14   14   14   16   20   22   24   25 
LCS_GDT     P     129     P     129      4    5   13     4    4    4    4    4    5    7    8   10   11   12   12   14   14   14   16   20   22   24   29 
LCS_GDT     C     130     C     130      4    5   13     4    4    4    4    4    5    7    8   10   11   12   12   13   13   13   15   15   16   17   23 
LCS_GDT     Q     131     Q     131      4    5   13     4    4    5    5    5    5    7    8    9   10   12   12   14   15   16   19   21   25   30   30 
LCS_GDT     W     161     W     161      4    5   13     3    3    4    5    5    5    5    5    5    5    5    6   10   12   13   13   13   15   15   15 
LCS_GDT     G     162     G     162      4    5   13     4    4    4    5    5    5    5    7    8   11   12   12   12   13   13   14   14   15   15   17 
LCS_GDT     L     163     L     163      4    5   13     4    4    4    5    5    5    5    7   10   11   12   12   13   13   13   14   14   15   15   17 
LCS_GDT     T     164     T     164      4    5   13     4    4    4    5    5    5    6    7   10   11   12   12   13   13   13   14   14   15   15   17 
LCS_GDT     V     165     V     165      4    5   13     4    4    4    5    5    5    6    7   10   11   11   11   13   13   13   14   14   15   15   16 
LCS_GDT     A     220     A     220      4    5   14     3    3    5    5    5    5    6    7    8    9    9   11   11   12   13   14   14   15   15   16 
LCS_GDT     L     221     L     221      4    6   14     3    4    5    5    6    7    8    9   11   11   12   12   13   13   13   14   14   15   15   16 
LCS_GDT     G     222     G     222      4    6   14     3    4    5    5    6    7    8   10   11   11   12   12   13   13   13   14   14   15   15   16 
LCS_GDT     A     223     A     223      4    6   14     3    4    5    5    6    7    8   10   11   11   12   12   13   13   13   14   14   15   15   16 
LCS_GDT     D     224     D     224      4    6   14     3    4    5    5    6    6    7   10   11   11   12   12   13   13   13   14   14   15   15   16 
LCS_GDT     P     225     P     225      3    6   14     3    3    3    5    6    6    7   10   11   11   12   12   13   13   13   14   14   15   16   17 
LCS_GDT     A     226     A     226      3    6   14     1    3    3    5    6    7    8   10   11   11   12   12   13   13   13   14   14   15   15   16 
LCS_GDT     T     227     T     227      3    4   14     1    3    3    3    4    5    7    7    8    9    9   11   11   12   13   14   14   15   15   16 
LCS_GDT     T     233     T     233      7    8   31     3    6    7    8    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     P     234     P     234      7    8   31     5    6    7    8    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     V     235     V     235      7    8   31     5    6    7    8    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     P     236     P     236      7    8   31     5    6    7    8    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     D     237     D     237      7   13   31     5    6    7    8   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     T     238     T     238      7   13   31     4    6    7    7    9   11   13   20   21   24   26   27   28   28   31   31   31   31   31   32 
LCS_GDT     L     239     L     239      7   13   31     5    6    7    9   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     S     240     S     240     10   13   31     5   10   10   10   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     E     241     E     241     10   13   31     5   10   10   10   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     Y     242     Y     242     10   13   31     5   10   10   10   12   12   14   15   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     A     243     A     243     10   13   31     6   10   10   10   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     F     244     F     244     10   13   31     6   10   10   10   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     A     245     A     245     10   13   31     6   10   10   10   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     G     246     G     246     10   13   31     5   10   10   10   12   12   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     L     247     L     247     10   13   31     6   10   10   10   12   12   14   16   20   22   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     L     248     L     248     10   13   31     6   10   10   10   12   12   14   16   20   22   25   27   28   29   31   31   31   31   31   32 
LCS_GDT     R     249     R     249     10   13   31     6   10   10   10   12   12   14   20   20   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     G     250     G     250      4   11   31     3    4    4    4    6   10   14   15   18   21   25   25   27   28   31   31   31   31   31   32 
LCS_GDT     T     251     T     251      4    5   31     3    4    4    6    9   10   14   20   20   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     K     252     K     252      4    5   31     3    4    5    6    9   10   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     T     253     T     253      4    4   31     3    4    4    4    4    6   13   16   18   21   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     E     254     E     254      3    3   31     3    4    5    6    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     V     255     V     255      3    3   31     3    3    5    8    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     V     256     V     256      3    3   31     0    3    3    3    3    6    8   12   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     K     257     K     257      3    3   31     0    3    3    8    9   11   14   17   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     G     275     G     275      3    6   31     3    4    4    6    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     Y     276     Y     276      5    6   31     3    3    5    8    9   11   14   20   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     I     277     I     277      5    6   31     3    4    5    5    6    6    9   13   21   24   26   27   28   29   31   31   31   31   31   32 
LCS_GDT     E     278     E     278      5    6   31     3    4    5    5    6    6    7    9   12   15   24   25   28   29   31   31   31   31   31   32 
LCS_GDT     Q     279     Q     279      5    6   31     3    4    5    5    6    6    7    7   11   14   18   21   26   29   31   31   31   31   31   32 
LCS_GDT     G     280     G     280      5    6   31     3    4    5    5    6    6    7    8   11   13   18   21   26   29   31   31   31   31   31   32 
LCS_GDT     E     281     E     281      3    3   11     3    3    3    3    3    4    4    4    8    8    8    9   11   12   14   24   25   25   31   32 
LCS_AVERAGE  LCS_A:   6.19  (   2.78    3.68   12.11 )

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      6     10     10     10     12     12     14     20     21     24     26     27     28     29     31     31     31     31     31     32 
GDT PERCENT_CA   3.13   5.21   5.21   5.21   6.25   6.25   7.29  10.42  10.94  12.50  13.54  14.06  14.58  15.10  16.15  16.15  16.15  16.15  16.15  16.67
GDT RMS_LOCAL    0.32   0.66   0.66   0.66   1.38   1.38   2.68   3.29   3.36   3.62   3.86   3.99   4.16   4.56   4.74   4.74   4.74   4.74   4.74   5.21
GDT RMS_ALL_CA  30.45  29.57  29.57  29.57  29.91  29.91  18.76  19.00  19.11  19.25  19.35  19.43  19.45  19.49  19.48  19.48  19.48  19.48  19.48  19.49

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122         40.956
LGA    K     123      K     123         37.432
LGA    R     124      R     124         32.159
LGA    L     125      L     125         31.470
LGA    R     126      R     126         30.816
LGA    G     127      G     127         23.564
LGA    A     128      A     128         20.108
LGA    P     129      P     129         19.165
LGA    C     130      C     130         18.239
LGA    Q     131      Q     131         15.232
LGA    W     161      W     161         20.637
LGA    G     162      G     162         21.762
LGA    L     163      L     163         22.281
LGA    T     164      T     164         25.063
LGA    V     165      V     165         27.720
LGA    A     220      A     220         40.205
LGA    L     221      L     221         37.853
LGA    G     222      G     222         34.704
LGA    A     223      A     223         31.439
LGA    D     224      D     224         30.664
LGA    P     225      P     225         26.603
LGA    A     226      A     226         25.277
LGA    T     227      T     227         23.400
LGA    T     233      T     233          3.925
LGA    P     234      P     234          3.913
LGA    V     235      V     235          3.253
LGA    P     236      P     236          1.979
LGA    D     237      D     237          2.247
LGA    T     238      T     238          3.777
LGA    L     239      L     239          2.126
LGA    S     240      S     240          3.996
LGA    E     241      E     241          3.654
LGA    Y     242      Y     242          5.098
LGA    A     243      A     243          3.835
LGA    F     244      F     244          3.096
LGA    A     245      A     245          3.607
LGA    G     246      G     246          3.358
LGA    L     247      L     247          5.702
LGA    L     248      L     248          6.619
LGA    R     249      R     249          3.886
LGA    G     250      G     250          7.494
LGA    T     251      T     251          3.945
LGA    K     252      K     252          3.034
LGA    T     253      T     253          5.870
LGA    E     254      E     254          0.649
LGA    V     255      V     255          3.441
LGA    V     256      V     256          5.547
LGA    K     257      K     257          5.456
LGA    G     275      G     275          2.742
LGA    Y     276      Y     276          3.183
LGA    I     277      I     277          5.724
LGA    E     278      E     278          8.121
LGA    Q     279      Q     279          9.810
LGA    G     280      G     280         10.855
LGA    E     281      E     281         16.297

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   55  192    4.0     20    3.29     9.245     7.856     0.590

LGA_LOCAL      RMSD =  3.292  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 19.003  Number of atoms =   55 
Std_ALL_ATOMS  RMSD = 16.324  (standard rmsd on all 55 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.610748 * X  +   0.735997 * Y  +   0.292053 * Z  +  39.108501
  Y_new =   0.762753 * X  +  -0.645870 * Y  +   0.032558 * Z  +  86.293129
  Z_new =   0.212591 * X  +   0.202880 * Y  +  -0.955848 * Z  +  77.658409 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.932446   -0.209147  [ DEG:   168.0168    -11.9832 ]
  Theta =  -0.214225   -2.927367  [ DEG:   -12.2742   -167.7258 ]
  Phi   =   0.895619   -2.245974  [ DEG:    51.3152   -128.6848 ]
 
# 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: T0356TS464_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_4-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   55  192   4.0   20   3.29   7.856    16.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_4-D2
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM     59  CA  THR   122      75.156  63.013 109.990  1.00  0.00
ATOM     60  CA  LYS   123      78.342  64.936 109.181  1.00  0.00
ATOM     61  CA  ARG   124      77.504  64.694 105.468  1.00  0.00
ATOM     62  CA  LEU   125      74.124  66.400 105.901  1.00  0.00
ATOM     63  CA  ARG   126      75.556  69.281 107.950  1.00  0.00
ATOM     64  CA  GLY   127      78.373  69.649 105.409  1.00  0.00
ATOM     65  CA  ALA   128      75.817  70.110 102.613  1.00  0.00
ATOM     66  CA  PRO   129      73.547  72.204 104.846  1.00  0.00
ATOM     67  CA  CYS   130      76.408  74.613 105.567  1.00  0.00
ATOM     68  CA  GLN   131      77.009  74.871 101.807  1.00  0.00
ATOM     69  CA  TRP   161      65.293  73.249 102.108  1.00  0.00
ATOM     70  CA  GLY   162      62.196  71.307 101.030  1.00  0.00
ATOM     71  CA  LEU   163      62.343  69.300  97.810  1.00  0.00
ATOM     72  CA  THR   164      59.364  67.456  96.344  1.00  0.00
ATOM     73  CA  VAL   165      60.037  63.731  96.612  1.00  0.00
ATOM     74  CA  ALA   220      48.570  67.564  56.692  1.00  0.00
ATOM     75  CA  LEU   221      49.452  70.778  58.494  1.00  0.00
ATOM     76  CA  GLY   222      53.231  70.791  58.013  1.00  0.00
ATOM     77  CA  ALA   223      54.687  67.753  59.811  1.00  0.00
ATOM     78  CA  ASP   224      57.136  65.671  57.756  1.00  0.00
ATOM     79  CA  PRO   225      57.255  62.922  60.341  1.00  0.00
ATOM     80  CA  ALA   226      55.467  61.740  63.476  1.00  0.00
ATOM     81  CA  THR   227      57.298  60.814  66.657  1.00  0.00
ATOM     82  CA  THR   233      66.717  67.278  66.819  1.00  0.00
ATOM     83  CA  PRO   234      68.246  65.284  63.937  1.00  0.00
ATOM     84  CA  VAL   235      71.679  66.388  62.695  1.00  0.00
ATOM     85  CA  PRO   236      75.054  65.145  61.332  1.00  0.00
ATOM     86  CA  ASP   237      77.235  63.102  63.699  1.00  0.00
ATOM     87  CA  THR   238      80.349  65.294  63.303  1.00  0.00
ATOM     88  CA  LEU   239      78.325  68.146  64.843  1.00  0.00
ATOM     89  CA  SER   240      78.508  71.907  65.504  1.00  0.00
ATOM     90  CA  GLU   241      79.916  71.552  69.043  1.00  0.00
ATOM     91  CA  TYR   242      80.661  75.293  68.751  1.00  0.00
ATOM     92  CA  ALA   243      77.019  76.383  68.334  1.00  0.00
ATOM     93  CA  PHE   244      76.261  74.529  71.592  1.00  0.00
ATOM     94  CA  ALA   245      78.271  77.334  73.234  1.00  0.00
ATOM     95  CA  GLY   246      75.753  80.166  72.705  1.00  0.00
ATOM     96  CA  LEU   247      73.020  77.549  73.250  1.00  0.00
ATOM     97  CA  LEU   248      74.106  77.250  76.906  1.00  0.00
ATOM     98  CA  ARG   249      75.229  80.879  77.357  1.00  0.00
ATOM     99  CA  GLY   250      78.773  79.454  77.179  1.00  0.00
ATOM    100  CA  THR   251      81.712  80.179  74.848  1.00  0.00
ATOM    101  CA  LYS   252      84.371  78.148  72.999  1.00  0.00
ATOM    102  CA  THR   253      86.816  78.082  75.933  1.00  0.00
ATOM    103  CA  GLU   254      84.222  76.948  78.499  1.00  0.00
ATOM    104  CA  VAL   255      82.666  74.285  76.236  1.00  0.00
ATOM    105  CA  VAL   256      86.211  72.918  75.807  1.00  0.00
ATOM    106  CA  LYS   257      87.596  73.653  79.291  1.00  0.00
ATOM    107  CA  GLY   275      87.469  56.294  86.035  1.00  0.00
ATOM    108  CA  TYR   276      83.746  56.991  85.067  1.00  0.00
ATOM    109  CA  ILE   277      83.115  56.671  81.349  1.00  0.00
ATOM    110  CA  GLU   278      84.628  54.379  78.760  1.00  0.00
ATOM    111  CA  GLN   279      84.237  53.841  75.023  1.00  0.00
ATOM    112  CA  GLY   280      83.135  50.567  73.519  1.00  0.00
ATOM    113  CA  GLU   281      83.135  51.316  69.815  1.00  0.00
TER
END
