
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0372AL333_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   33 , name T0372_D2.pdb
# PARAMETERS: T0372AL333_1-D2.T0372_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:    16       118 - 142         4.74    20.10
  LCS_AVERAGE:      8.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       227 - 231         1.69    19.71
  LONGEST_CONTINUOUS_SEGMENT:     5       247 - 252         0.33    26.03
  LCS_AVERAGE:      2.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       247 - 252         0.33    26.03
  LCS_AVERAGE:      1.87

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:  172
LCS_GDT     R     118     R     118      3    3   16     0    3    3    3    6    6    9    9   13   14   15   15   15   15   17   18   19   20   22   22 
LCS_GDT     A     119     A     119      3    3   16     1    3    3    4    6    6    9    9   13   14   15   15   17   17   19   20   20   22   22   22 
LCS_GDT     Y     120     Y     120      3    3   16     0    3    3    5    6    6    7    9   13   14   15   15   17   17   19   20   20   22   22   22 
LCS_GDT     A     121     A     121      3    3   16     3    3    4    5    6    6    7    9   13   14   15   15   17   17   19   20   20   22   22   22 
LCS_GDT     I     124     I     124      3    3   16     3    3    3    3    4    7    9    9   13   14   15   15   17   17   19   20   20   22   22   22 
LCS_GDT     Y     125     Y     125      3    3   16     3    3    3    3    4    7    9    9   13   14   15   15   15   16   18   18   19   22   22   22 
LCS_GDT     L     126     L     126      3    3   16     3    3    3    3    4    7    9    9   13   14   15   15   15   15   17   18   19   20   20   20 
LCS_GDT     K     134     K     134      0    4   16     0    2    3    4    6    7    9    9   13   14   15   15   15   16   17   18   19   20   21   21 
LCS_GDT     G     135     G     135      3    4   16     0    3    3    4    6    7    9    9   13   14   15   15   15   16   17   17   18   20   21   21 
LCS_GDT     K     136     K     136      3    4   16     0    3    3    3    6    7    9    9   13   14   15   15   15   15   17   17   18   19   21   21 
LCS_GDT     K     137     K     137      3    4   16     3    3    4    4    6    7    9    9   13   14   15   15   15   15   15   16   17   19   21   21 
LCS_GDT     F     138     F     138      3    4   16     3    3    3    4    4    5    8    9   13   14   15   15   15   15   15   15   17   19   21   21 
LCS_GDT     Q     139     Q     139      3    4   16     3    3    3    4    4    5    6    9   10   14   15   15   15   15   15   15   16   16   16   17 
LCS_GDT     A     140     A     140      3    4   16     3    3    3    4    4    5    8    9   13   14   15   15   15   15   15   15   16   16   16   17 
LCS_GDT     K     141     K     141      3    4   16     3    3    3    4    4    5    6    9   10   14   15   15   15   15   15   15   16   16   16   17 
LCS_GDT     R     142     R     142      3    3   16     3    3    3    3    4    4    4    5    6    7    9    9   11   11   12   15   16   16   16   17 
LCS_GDT     P     225     P     225      3    4   13     3    3    3    4    4    4    7    8    9   10   11   12   17   17   19   20   20   22   22   22 
LCS_GDT     I     226     I     226      3    4   13     3    3    3    4    4    5    7    8    9   10   11   14   17   17   19   20   20   22   22   22 
LCS_GDT     N     227     N     227      3    5   13     3    3    4    5    5    5    6    8    9   10   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     H     228     H     228      3    5   13     3    3    3    4    5    5    6    8    8   10   11   14   17   17   19   20   20   22   22   22 
LCS_GDT     E     229     E     229      3    5   13     3    3    3    4    5    5    6    8    8   10   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     T     230     T     230      3    5   13     3    3    3    4    5    5    6    8    8   10   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     F     231     F     231      3    5   13     0    3    3    4    5    5    7    9   10   11   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     G     232     G     232      3    3   13     3    3    3    3    4    5    7    8   10   11   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     V     233     V     233      3    4   13     3    3    4    5    5    6    7    9   10   11   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     H     234     H     234      3    4   13     3    3    4    5    6    6    7    9   10   11   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     V     235     V     235      3    4   13     3    3    4    5    6    6    7    9   10   11   11   13   14   16   19   20   20   22   22   22 
LCS_GDT     E     236     E     236      3    4   13     3    3    4    5    6    6    7    9   10   11   11   13   14   16   18   18   20   22   22   22 
LCS_GDT     A     247     A     247      5    5   13     5    5    5    5    5    5    5    5    6    6    6    8   13   15   19   20   20   22   22   22 
LCS_GDT     M     248     M     248      5    5   10     5    5    5    5    5    5    5    5    6    6    6    8   10   13   18   20   20   22   22   22 
LCS_GDT     N     250     N     250      5    5   10     5    5    5    5    5    5    6    7    8   10   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     Y     251     Y     251      5    5   10     5    5    5    5    5    5    6    6    7   10   12   14   17   17   19   20   20   22   22   22 
LCS_GDT     E     252     E     252      5    5   10     5    5    5    5    5    5    6    6    8   10   12   14   17   17   19   20   20   22   22   22 
LCS_AVERAGE  LCS_A:   4.13  (   1.87    2.34    8.19 )

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      5      5      5      5      6      7      9      9     13     14     15     15     17     17     19     20     20     22     22     22 
GDT PERCENT_CA   2.91   2.91   2.91   2.91   3.49   4.07   5.23   5.23   7.56   8.14   8.72   8.72   9.88   9.88  11.05  11.63  11.63  12.79  12.79  12.79
GDT RMS_LOCAL    0.33   0.33   0.33   0.33   2.03   2.42   2.68   2.68   3.56   3.83   3.99   3.99   4.97   4.97   5.43   5.57   5.57   6.10   6.10   6.10
GDT RMS_ALL_CA  26.03  26.03  26.03  26.03  11.84  21.47  22.33  22.33  21.47  21.14  20.74  20.74  16.89  16.89  16.54  16.61  16.61  16.19  16.19  16.19

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          1.587
LGA    A     119      A     119          3.416
LGA    Y     120      Y     120          5.280
LGA    A     121      A     121          4.945
LGA    I     124      I     124          2.826
LGA    Y     125      Y     125          3.382
LGA    L     126      L     126          3.419
LGA    K     134      K     134          2.052
LGA    G     135      G     135          2.433
LGA    K     136      K     136          1.961
LGA    K     137      K     137          2.761
LGA    F     138      F     138          6.213
LGA    Q     139      Q     139          9.876
LGA    A     140      A     140          8.672
LGA    K     141      K     141         10.991
LGA    R     142      R     142         17.881
LGA    P     225      P     225         32.278
LGA    I     226      I     226         27.850
LGA    N     227      N     227         29.879
LGA    H     228      H     228         32.868
LGA    E     229      E     229         26.694
LGA    T     230      T     230         23.319
LGA    F     231      F     231         27.370
LGA    G     232      G     232         26.004
LGA    V     233      V     233         23.660
LGA    H     234      H     234         25.425
LGA    V     235      V     235         29.845
LGA    E     236      E     236         30.299
LGA    A     247      A     247         29.946
LGA    M     248      M     248         36.097
LGA    N     250      N     250         34.066
LGA    Y     251      Y     251         36.913
LGA    E     252      E     252         43.291

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  172    4.0      9    2.68     5.669     4.992     0.324

LGA_LOCAL      RMSD =  2.679  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 22.600  Number of atoms =   33 
Std_ALL_ATOMS  RMSD = 11.129  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.629629 * X  +   0.148385 * Y  +   0.762594 * Z  + -26.510612
  Y_new =   0.651211 * X  +   0.434489 * Y  +  -0.622209 * Z  + -11.149282
  Z_new =  -0.423665 * X  +   0.888370 * Y  +   0.176937 * Z  +   8.385068 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.374199   -1.767394  [ DEG:    78.7358   -101.2642 ]
  Theta =   0.437488    2.704105  [ DEG:    25.0662    154.9338 ]
  Phi   =   0.802247   -2.339346  [ DEG:    45.9654   -134.0347 ]
 
# 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: T0372AL333_1-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  172   4.0    9   2.68   4.992    11.13
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_1-D2
REMARK Aligment from pdb entry: 1nu0_A
ATOM    293  N   ARG   118      22.315  39.693   7.931  1.00  0.00              
ATOM    294  CA  ARG   118      23.662  40.288   7.992  1.00  0.00              
ATOM    295  C   ARG   118      24.027  40.616   9.433  1.00  0.00              
ATOM    296  O   ARG   118      23.185  41.087  10.202  1.00  0.00              
ATOM    297  N   ALA   119      25.281  40.379   9.759  1.00  0.00              
ATOM    298  CA  ALA   119      25.811  40.770  11.085  1.00  0.00              
ATOM    299  C   ALA   119      25.759  42.302  11.209  1.00  0.00              
ATOM    300  O   ALA   119      25.988  43.043  10.224  1.00  0.00              
ATOM    301  N   TYR   120      25.509  42.790  12.419  1.00  0.00              
ATOM    302  CA  TYR   120      25.507  44.224  12.655  1.00  0.00              
ATOM    303  C   TYR   120      26.092  44.428  14.050  1.00  0.00              
ATOM    304  O   TYR   120      26.154  43.496  14.855  1.00  0.00              
ATOM    305  N   ALA   121      26.501  45.679  14.329  1.00  0.00              
ATOM    306  CA  ALA   121      27.024  46.012  15.663  1.00  0.00              
ATOM    307  C   ALA   121      25.932  46.212  16.695  1.00  0.00              
ATOM    308  O   ALA   121      25.011  47.019  16.486  1.00  0.00              
ATOM    309  N   ILE   124      26.030  45.497  17.800  1.00  0.00              
ATOM    310  CA  ILE   124      25.074  45.634  18.921  1.00  0.00              
ATOM    311  C   ILE   124      25.643  46.852  19.671  1.00  0.00              
ATOM    312  O   ILE   124      26.783  46.818  20.100  1.00  0.00              
ATOM    313  N   TYR   125      24.913  47.942  19.857  1.00  0.00              
ATOM    314  CA  TYR   125      25.660  49.013  20.508  1.00  0.00              
ATOM    315  C   TYR   125      25.962  48.821  21.978  1.00  0.00              
ATOM    316  O   TYR   125      25.308  48.051  22.682  1.00  0.00              
ATOM    317  N   LEU   126      27.028  49.492  22.404  1.00  0.00              
ATOM    318  CA  LEU   126      27.508  49.430  23.775  1.00  0.00              
ATOM    319  C   LEU   126      26.449  49.951  24.742  1.00  0.00              
ATOM    320  O   LEU   126      25.639  50.815  24.377  1.00  0.00              
ATOM    321  N   LYS   134      21.191  46.728  36.709  1.00  0.00              
ATOM    322  CA  LYS   134      20.769  47.153  38.036  1.00  0.00              
ATOM    323  C   LYS   134      19.266  47.353  38.089  1.00  0.00              
ATOM    324  O   LYS   134      18.776  48.479  38.039  1.00  0.00              
ATOM    325  N   GLY   135      18.539  46.247  38.219  1.00  0.00              
ATOM    326  CA  GLY   135      17.089  46.281  38.234  1.00  0.00              
ATOM    327  C   GLY   135      16.732  45.513  36.977  1.00  0.00              
ATOM    328  O   GLY   135      15.572  45.358  36.593  1.00  0.00              
ATOM    329  N   LYS   136      17.806  45.041  36.353  1.00  0.00              
ATOM    330  CA  LYS   136      17.845  44.252  35.123  1.00  0.00              
ATOM    331  C   LYS   136      16.960  42.993  35.130  1.00  0.00              
ATOM    332  O   LYS   136      16.826  42.298  36.147  1.00  0.00              
ATOM    333  N   LYS   137      16.380  42.681  33.978  1.00  0.00              
ATOM    334  CA  LYS   137      15.596  41.465  33.846  1.00  0.00              
ATOM    335  C   LYS   137      15.799  40.899  32.441  1.00  0.00              
ATOM    336  O   LYS   137      15.750  41.623  31.437  1.00  0.00              
ATOM    337  N   PHE   138      16.044  39.597  32.376  1.00  0.00              
ATOM    338  CA  PHE   138      16.263  38.938  31.094  1.00  0.00              
ATOM    339  C   PHE   138      15.459  37.636  30.952  1.00  0.00              
ATOM    340  O   PHE   138      15.187  36.956  31.937  1.00  0.00              
ATOM    341  N   GLN   139      15.074  37.299  29.725  1.00  0.00              
ATOM    342  CA  GLN   139      14.336  36.057  29.477  1.00  0.00              
ATOM    343  C   GLN   139      15.225  34.883  29.906  1.00  0.00              
ATOM    344  O   GLN   139      16.431  35.062  30.128  1.00  0.00              
ATOM    345  N   ALA   140      14.632  33.699  30.049  1.00  0.00              
ATOM    346  CA  ALA   140      15.435  32.543  30.394  1.00  0.00              
ATOM    347  C   ALA   140      16.340  32.310  29.192  1.00  0.00              
ATOM    348  O   ALA   140      15.992  32.669  28.036  1.00  0.00              
ATOM    349  N   LYS   141      17.503  31.729  29.484  1.00  0.00              
ATOM    350  CA  LYS   141      18.549  31.495  28.524  1.00  0.00              
ATOM    351  C   LYS   141      18.132  30.869  27.200  1.00  0.00              
ATOM    352  O   LYS   141      18.624  31.305  26.142  1.00  0.00              
ATOM    353  N   ARG   142      17.256  29.864  27.261  1.00  0.00              
ATOM    354  CA  ARG   142      16.798  29.164  26.052  1.00  0.00              
ATOM    355  C   ARG   142      16.109  30.112  25.088  1.00  0.00              
ATOM    356  O   ARG   142      16.299  30.028  23.870  1.00  0.00              
ATOM    357  N   PRO   225      15.298  31.029  25.609  1.00  0.00              
ATOM    358  CA  PRO   225      14.649  31.967  24.714  1.00  0.00              
ATOM    359  C   PRO   225      15.593  33.104  24.296  1.00  0.00              
ATOM    360  O   PRO   225      15.490  33.617  23.173  1.00  0.00              
ATOM    361  N   ILE   226      16.511  33.503  25.178  1.00  0.00              
ATOM    362  CA  ILE   226      17.477  34.548  24.845  1.00  0.00              
ATOM    363  C   ILE   226      18.304  34.040  23.658  1.00  0.00              
ATOM    364  O   ILE   226      18.607  34.785  22.706  1.00  0.00              
ATOM    365  N   ASN   227      18.635  32.739  23.673  1.00  0.00              
ATOM    366  CA  ASN   227      19.427  32.147  22.559  1.00  0.00              
ATOM    367  C   ASN   227      18.686  32.113  21.210  1.00  0.00              
ATOM    368  O   ASN   227      19.298  31.833  20.155  1.00  0.00              
ATOM    369  N   HIS   228      17.383  32.392  21.261  1.00  0.00              
ATOM    370  CA  HIS   228      16.538  32.461  20.055  1.00  0.00              
ATOM    371  C   HIS   228      16.233  33.878  19.634  1.00  0.00              
ATOM    372  O   HIS   228      15.465  34.074  18.735  1.00  0.00              
ATOM    373  N   GLU   229      16.876  34.856  20.251  1.00  0.00              
ATOM    374  CA  GLU   229      16.605  36.239  19.828  1.00  0.00              
ATOM    375  C   GLU   229      16.849  36.557  18.391  1.00  0.00              
ATOM    376  O   GLU   229      16.030  37.320  17.830  1.00  0.00              
ATOM    377  N   THR   230      17.912  36.004  17.780  1.00  0.00              
ATOM    378  CA  THR   230      18.158  36.292  16.378  1.00  0.00              
ATOM    379  C   THR   230      17.059  35.645  15.533  1.00  0.00              
ATOM    380  O   THR   230      16.645  36.200  14.515  1.00  0.00              
ATOM    381  N   PHE   231      16.503  34.514  15.974  1.00  0.00              
ATOM    382  CA  PHE   231      15.446  33.915  15.163  1.00  0.00              
ATOM    383  C   PHE   231      14.198  34.856  15.196  1.00  0.00              
ATOM    384  O   PHE   231      13.490  34.994  14.214  1.00  0.00              
ATOM    385  N   GLY   232      13.889  35.467  16.341  1.00  0.00              
ATOM    386  CA  GLY   232      12.758  36.389  16.408  1.00  0.00              
ATOM    387  C   GLY   232      13.031  37.575  15.458  1.00  0.00              
ATOM    388  O   GLY   232      12.154  38.005  14.746  1.00  0.00              
ATOM    389  N   VAL   233      14.258  38.090  15.459  1.00  0.00              
ATOM    390  CA  VAL   233      14.580  39.218  14.560  1.00  0.00              
ATOM    391  C   VAL   233      14.418  38.829  13.102  1.00  0.00              
ATOM    392  O   VAL   233      13.913  39.633  12.304  1.00  0.00              
ATOM    393  N   HIS   234      14.874  37.624  12.740  1.00  0.00              
ATOM    394  CA  HIS   234      14.715  37.150  11.390  1.00  0.00              
ATOM    395  C   HIS   234      13.239  37.141  11.017  1.00  0.00              
ATOM    396  O   HIS   234      12.842  37.591   9.949  1.00  0.00              
ATOM    397  N   VAL   235      12.404  36.605  11.900  1.00  0.00              
ATOM    398  CA  VAL   235      11.003  36.450  11.571  1.00  0.00              
ATOM    399  C   VAL   235      10.293  37.803  11.542  1.00  0.00              
ATOM    400  O   VAL   235       9.485  38.009  10.667  1.00  0.00              
ATOM    401  N   GLU   236      10.582  38.711  12.482  1.00  0.00              
ATOM    402  CA  GLU   236       9.962  40.030  12.453  1.00  0.00              
ATOM    403  C   GLU   236      10.404  40.746  11.150  1.00  0.00              
ATOM    404  O   GLU   236       9.556  41.396  10.478  1.00  0.00              
ATOM    405  N   ALA   247      11.667  40.609  10.773  1.00  0.00              
ATOM    406  CA  ALA   247      12.172  41.241   9.543  1.00  0.00              
ATOM    407  C   ALA   247      11.406  40.697   8.334  1.00  0.00              
ATOM    408  O   ALA   247      10.938  41.445   7.461  1.00  0.00              
ATOM    409  N   MET   248      11.286  39.373   8.277  1.00  0.00              
ATOM    410  CA  MET   248      10.616  38.728   7.173  1.00  0.00              
ATOM    411  C   MET   248       9.163  39.253   7.084  1.00  0.00              
ATOM    412  O   MET   248       8.672  39.592   6.000  1.00  0.00              
ATOM    413  N   ASN   250       7.851  42.079   8.435  1.00  0.00              
ATOM    414  CA  ASN   250       7.813  43.533   8.209  1.00  0.00              
ATOM    415  C   ASN   250       8.077  43.897   6.774  1.00  0.00              
ATOM    416  O   ASN   250       7.490  44.855   6.273  1.00  0.00              
ATOM    417  N   TYR   251       8.980  43.157   6.136  1.00  0.00              
ATOM    418  CA  TYR   251       9.335  43.422   4.752  1.00  0.00              
ATOM    419  C   TYR   251       8.249  42.943   3.821  1.00  0.00              
ATOM    420  O   TYR   251       8.366  43.094   2.592  1.00  0.00              
ATOM    421  N   GLU   252       7.194  42.358   4.384  1.00  0.00              
ATOM    422  CA  GLU   252       6.092  41.921   3.571  1.00  0.00              
ATOM    423  C   GLU   252       6.165  40.594   2.877  1.00  0.00              
ATOM    424  O   GLU   252       5.574  40.403   1.823  1.00  0.00              
END
