
#######################################################
#                                                     #
#                        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   22 (  165),  selected   17 , name T0296TS351_3
# Molecule2: number of CA atoms  414 ( 2974),  selected   17 , name T0296.pdb
# PARAMETERS: T0296TS351_3.T0296.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       424 - 439         4.80     5.23
  LONGEST_CONTINUOUS_SEGMENT:    16       425 - 440         4.77     5.24
  LCS_AVERAGE:      3.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       425 - 433         1.55    13.08
  LONGEST_CONTINUOUS_SEGMENT:     9       426 - 434         1.91    11.66
  LONGEST_CONTINUOUS_SEGMENT:     9       432 - 440         1.65     8.71
  LCS_AVERAGE:      2.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       426 - 433         0.89    13.06
  LCS_AVERAGE:      1.72

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:  414
LCS_GDT     A     424     A     424      4    8   16     3    4    4    4    6    7    8    9   10   11   11   13   13   14   16   17   17   17   17   17 
LCS_GDT     S     425     S     425      4    9   16     3    4    4    7    8    8    9   10   11   12   12   13   14   15   16   17   17   17   17   17 
LCS_GDT     S     426     S     426      8    9   16     6    7    7    8    8    8    9   10   11   12   12   13   14   15   16   17   17   17   17   17 
LCS_GDT     V     427     V     427      8    9   16     6    7    7    8    8    8    9   10   11   12   12   13   14   15   16   17   17   17   17   17 
LCS_GDT     D     428     D     428      8    9   16     6    7    7    8    8    8    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     F     429     F     429      8    9   16     6    7    7    8    8    8    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     I     430     I     430      8    9   16     6    7    7    8    8    8    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     S     431     S     431      8    9   16     6    7    7    8    8    8    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     R     432     R     432      8    9   16     6    7    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     G     433     G     433      8    9   16     3    4    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     G     434     G     434      7    9   16     4    6    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     Q     435     Q     435      7    9   16     4    6    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     I     436     I     436      7    9   16     3    6    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     P     437     P     437      7    9   16     3    6    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     A     438     A     438      7    9   16     3    6    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     P     439     P     439      7    9   16     4    6    7    8    9    9    9   10   11   12   13   13   14   15   16   17   17   17   17   17 
LCS_GDT     I     440     I     440      7    9   16     4    6    7    8    9    9    9   10   10   12   13   13   13   14   16   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   2.58  (   1.72    2.16    3.86 )

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      7      7      8      9      9      9     10     11     12     13     13     14     15     16     17     17     17     17     17 
GDT PERCENT_CA   1.45   1.69   1.69   1.93   2.17   2.17   2.17   2.42   2.66   2.90   3.14   3.14   3.38   3.62   3.86   4.11   4.11   4.11   4.11   4.11
GDT RMS_LOCAL    0.29   0.44   0.44   0.89   1.65   1.65   1.55   2.11   2.74   3.10   3.44   3.44   4.27   4.49   4.77   5.10   5.10   5.10   5.10   5.10
GDT RMS_ALL_CA  12.73  12.98  12.98  13.06   8.71   8.71  13.08  11.82   9.64   6.71   6.40   6.40   5.19   5.26   5.24   5.10   5.10   5.10   5.10   5.10

#      Molecule1      Molecule2       DISTANCE
LGA    A     424      A     424          7.633
LGA    S     425      S     425          3.585
LGA    S     426      S     426          2.248
LGA    V     427      V     427          2.320
LGA    D     428      D     428          1.888
LGA    F     429      F     429          0.761
LGA    I     430      I     430          1.422
LGA    S     431      S     431          1.522
LGA    R     432      R     432          0.787
LGA    G     433      G     433          2.870
LGA    G     434      G     434          3.529
LGA    Q     435      Q     435          6.142
LGA    I     436      I     436         10.454
LGA    P     437      P     437         14.561
LGA    A     438      A     438         16.947
LGA    P     439      P     439         20.651
LGA    I     440      I     440         25.997

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  414    4.0     10    2.11     2.536     2.416     0.453

LGA_LOCAL      RMSD =  2.109  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.460  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  5.102  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.261808 * X  +   0.644648 * Y  +  -0.718252 * Z  +  61.175964
  Y_new =  -0.657246 * X  +  -0.664062 * Y  +  -0.356440 * Z  +  24.999607
  Z_new =  -0.706742 * X  +   0.378749 * Y  +   0.597549 * Z  +  32.023064 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.564929   -2.576663  [ DEG:    32.3681   -147.6319 ]
  Theta =   0.784882    2.356711  [ DEG:    44.9704    135.0296 ]
  Phi   =  -1.949872    1.191721  [ DEG:  -111.7194     68.2806 ]
 
# 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: T0296TS351_3                                  
REMARK     2: T0296.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0296TS351_3.T0296.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  414   4.0   10   2.11   2.416     5.10
REMARK  ---------------------------------------------------------- 
MOLECULE T0296TS351_3
PFRMAT TS
TARGET T0296
MODEL  3  REFINED
PARENT N/A
ATOM      1  N   ALA   424      34.169   7.385  55.224  1.00  0.00
ATOM      2  CA  ALA   424      33.534   8.360  56.098  1.00  0.00
ATOM      3  C   ALA   424      33.290   9.706  55.344  1.00  0.00
ATOM      4  O   ALA   424      33.394   9.784  54.106  1.00  0.00
ATOM      5  CB  ALA   424      34.470   8.508  57.317  1.00  0.00
ATOM      6  N   SER   425      32.629  10.638  56.035  1.00  0.00
ATOM      7  CA  SER   425      32.319  11.960  55.509  1.00  0.00
ATOM      8  C   SER   425      33.625  12.693  55.129  1.00  0.00
ATOM      9  O   SER   425      34.471  13.002  55.954  1.00  0.00
ATOM     10  CB  SER   425      31.539  12.718  56.571  1.00  0.00
ATOM     11  OG  SER   425      31.974  12.627  57.911  1.00  0.00
ATOM     12  N   SER   426      33.680  13.028  53.853  1.00  0.00
ATOM     13  CA  SER   426      34.770  13.759  53.220  1.00  0.00
ATOM     14  C   SER   426      34.962  15.188  53.793  1.00  0.00
ATOM     15  O   SER   426      36.092  15.656  53.775  1.00  0.00
ATOM     16  CB  SER   426      34.502  13.808  51.710  1.00  0.00
ATOM     17  OG  SER   426      34.764  12.611  50.950  1.00  0.00
ATOM     18  N   VAL   427      33.907  15.988  54.051  1.00  0.00
ATOM     19  CA  VAL   427      34.004  17.317  54.660  1.00  0.00
ATOM     20  C   VAL   427      34.944  17.291  55.914  1.00  0.00
ATOM     21  O   VAL   427      35.765  18.204  56.060  1.00  0.00
ATOM     22  CB  VAL   427      32.575  17.781  55.011  1.00  0.00
ATOM     23  CG1 VAL   427      32.607  19.176  55.663  1.00  0.00
ATOM     24  CG2 VAL   427      31.680  17.860  53.761  1.00  0.00
ATOM     25  N   ASP   428      34.609  16.452  56.911  1.00  0.00
ATOM     26  CA  ASP   428      35.377  16.235  58.138  1.00  0.00
ATOM     27  C   ASP   428      36.776  15.599  57.839  1.00  0.00
ATOM     28  O   ASP   428      37.722  16.032  58.497  1.00  0.00
ATOM     29  CB  ASP   428      34.536  15.305  59.014  1.00  0.00
ATOM     30  CG  ASP   428      34.795  15.370  60.518  1.00  0.00
ATOM     31  OD1 ASP   428      35.915  15.252  60.996  1.00  0.00
ATOM     32  OD2 ASP   428      33.828  15.414  61.325  1.00  0.00
ATOM     33  N   PHE   429      36.878  14.562  56.998  1.00  0.00
ATOM     34  CA  PHE   429      38.122  13.928  56.544  1.00  0.00
ATOM     35  C   PHE   429      39.096  14.962  55.878  1.00  0.00
ATOM     36  O   PHE   429      40.277  14.970  56.199  1.00  0.00
ATOM     37  CB  PHE   429      37.792  12.799  55.554  1.00  0.00
ATOM     38  CG  PHE   429      38.929  11.867  55.203  1.00  0.00
ATOM     39  CD1 PHE   429      39.558  11.114  56.193  1.00  0.00
ATOM     40  CD2 PHE   429      39.387  11.790  53.886  1.00  0.00
ATOM     41  CE1 PHE   429      40.641  10.299  55.857  1.00  0.00
ATOM     42  CE2 PHE   429      40.471  10.972  53.560  1.00  0.00
ATOM     43  CZ  PHE   429      41.101  10.226  54.546  1.00  0.00
ATOM     44  N   ILE   430      38.563  15.866  55.059  1.00  0.00
ATOM     45  CA  ILE   430      39.273  16.971  54.416  1.00  0.00
ATOM     46  C   ILE   430      39.771  17.908  55.544  1.00  0.00
ATOM     47  O   ILE   430      40.940  18.299  55.433  1.00  0.00
ATOM     48  CB  ILE   430      38.394  17.679  53.335  1.00  0.00
ATOM     49  CG1 ILE   430      38.185  16.729  52.119  1.00  0.00
ATOM     50  CG2 ILE   430      39.091  19.001  52.856  1.00  0.00
ATOM     51  CD1 ILE   430      37.014  17.196  51.226  1.00  0.00
ATOM     52  N   SER   431      38.928  18.462  56.415  1.00  0.00
ATOM     53  CA  SER   431      39.379  19.256  57.513  1.00  0.00
ATOM     54  C   SER   431      40.486  18.580  58.338  1.00  0.00
ATOM     55  O   SER   431      41.402  19.312  58.702  1.00  0.00
ATOM     56  CB  SER   431      38.162  19.687  58.363  1.00  0.00
ATOM     57  OG  SER   431      37.355  20.754  57.904  1.00  0.00
ATOM     58  N   ARG   432      40.241  17.399  58.863  1.00  0.00
ATOM     59  CA  ARG   432      41.228  16.664  59.636  1.00  0.00
ATOM     60  C   ARG   432      42.628  16.670  58.958  1.00  0.00
ATOM     61  O   ARG   432      43.567  17.059  59.651  1.00  0.00
ATOM     62  CB  ARG   432      40.719  15.214  59.847  1.00  0.00
ATOM     63  CG  ARG   432      41.675  14.390  60.705  1.00  0.00
ATOM     64  CD  ARG   432      41.533  14.645  62.204  1.00  0.00
ATOM     65  NE  ARG   432      42.099  13.542  62.985  1.00  0.00
ATOM     66  CZ  ARG   432      42.587  13.640  64.226  1.00  0.00
ATOM     67  NH1 ARG   432      42.602  14.813  64.873  1.00  0.00
ATOM     68  NH2 ARG   432      43.084  12.600  64.908  1.00  0.00
ATOM     69  N   GLY   433      42.766  16.222  57.694  1.00  0.00
ATOM     70  CA  GLY   433      44.048  16.172  56.987  1.00  0.00
ATOM     71  C   GLY   433      44.570  17.544  56.534  1.00  0.00
ATOM     72  O   GLY   433      45.729  17.592  56.128  1.00  0.00
ATOM     73  N   GLY   434      43.701  18.556  56.343  1.00  0.00
ATOM     74  CA  GLY   434      44.119  19.830  55.822  1.00  0.00
ATOM     75  C   GLY   434      44.467  19.758  54.303  1.00  0.00
ATOM     76  O   GLY   434      45.480  20.338  53.889  1.00  0.00
ATOM     77  N   GLN   435      43.732  18.916  53.566  1.00  0.00
ATOM     78  CA  GLN   435      43.903  18.677  52.190  1.00  0.00
ATOM     79  C   GLN   435      42.608  19.049  51.422  1.00  0.00
ATOM     80  O   GLN   435      41.605  19.478  52.009  1.00  0.00
ATOM     81  CB  GLN   435      44.442  17.230  51.947  1.00  0.00
ATOM     82  CG  GLN   435      45.837  17.129  51.303  1.00  0.00
ATOM     83  CD  GLN   435      46.865  16.270  52.108  1.00  0.00
ATOM     84  OE1 GLN   435      47.034  15.070  51.836  1.00  0.00
ATOM     85  NE2 GLN   435      47.574  16.808  53.087  1.00  0.00
ATOM     86  N   ILE   436      42.782  19.276  50.135  1.00  0.00
ATOM     87  CA  ILE   436      41.630  19.605  49.331  1.00  0.00
ATOM     88  C   ILE   436      41.244  18.471  48.325  1.00  0.00
ATOM     89  O   ILE   436      42.193  17.994  47.654  1.00  0.00
ATOM     90  CB  ILE   436      41.875  20.889  48.474  1.00  0.00
ATOM     91  CG1 ILE   436      43.130  20.695  47.617  1.00  0.00
ATOM     92  CG2 ILE   436      42.032  22.104  49.382  1.00  0.00
ATOM     93  CD1 ILE   436      43.399  21.827  46.648  1.00  0.00
ATOM     94  N   PRO   437      39.974  17.821  48.273  1.00  0.00
ATOM     95  CA  PRO   437      39.862  16.878  47.241  1.00  0.00
ATOM     96  C   PRO   437      40.162  17.467  45.821  1.00  0.00
ATOM     97  O   PRO   437      39.845  18.638  45.504  1.00  0.00
ATOM     98  CB  PRO   437      38.433  16.341  47.275  1.00  0.00
ATOM     99  CG  PRO   437      37.659  17.609  47.698  1.00  0.00
ATOM    100  CD  PRO   437      38.556  18.228  48.709  1.00  0.00
ATOM    101  N   ALA   438      40.462  16.515  44.917  1.00  0.00
ATOM    102  CA  ALA   438      40.839  16.780  43.534  1.00  0.00
ATOM    103  C   ALA   438      39.587  17.182  42.804  1.00  0.00
ATOM    104  O   ALA   438      38.674  16.369  42.753  1.00  0.00
ATOM    105  CB  ALA   438      41.485  15.506  42.932  1.00  0.00
ATOM    106  N   PRO   439      39.366  18.420  42.298  1.00  0.00
ATOM    107  CA  PRO   439      38.077  18.700  41.618  1.00  0.00
ATOM    108  C   PRO   439      37.680  17.676  40.562  1.00  0.00
ATOM    109  O   PRO   439      38.503  16.987  39.932  1.00  0.00
ATOM    110  CB  PRO   439      38.113  20.147  41.085  1.00  0.00
ATOM    111  CG  PRO   439      39.227  20.729  42.014  1.00  0.00
ATOM    112  CD  PRO   439      40.270  19.603  42.104  1.00  0.00
ATOM    113  N   ILE   440      36.331  17.603  40.417  1.00  0.00
ATOM    114  CA  ILE   440      35.589  16.676  39.551  1.00  0.00
ATOM    115  C   ILE   440      36.103  16.697  38.064  1.00  0.00
ATOM    116  O   ILE   440      36.081  15.624  37.410  1.00  0.00
ATOM    117  CB  ILE   440      34.032  16.918  39.592  1.00  0.00
ATOM    118  CG1 ILE   440      33.426  16.445  40.911  1.00  0.00
ATOM    119  CG2 ILE   440      33.319  16.309  38.328  1.00  0.00
ATOM    120  CD1 ILE   440      31.968  16.966  41.192  1.00  0.00
ATOM    121  N   HIS   441      36.439  17.850  37.481  1.00  0.00
ATOM    122  CA  HIS   441      36.932  17.940  36.102  1.00  0.00
ATOM    123  C   HIS   441      38.187  17.037  35.823  1.00  0.00
ATOM    124  O   HIS   441      38.356  16.678  34.656  1.00  0.00
ATOM    125  CB  HIS   441      37.274  19.403  35.818  1.00  0.00
ATOM    126  CG  HIS   441      37.123  19.830  34.373  1.00  0.00
ATOM    127  ND1 HIS   441      35.965  19.615  33.630  1.00  0.00
ATOM    128  CD2 HIS   441      37.948  20.562  33.594  1.00  0.00
ATOM    129  CE1 HIS   441      36.103  20.222  32.468  1.00  0.00
ATOM    130  NE2 HIS   441      37.319  20.822  32.420  1.00  0.00
ATOM    131  N   SER   442      39.093  16.779  36.780  1.00  0.00
ATOM    132  CA  SER   442      40.318  15.994  36.567  1.00  0.00
ATOM    133  C   SER   442      40.086  14.487  36.224  1.00  0.00
ATOM    134  O   SER   442      40.990  13.887  35.627  1.00  0.00
ATOM    135  CB  SER   442      41.126  16.021  37.858  1.00  0.00
ATOM    136  OG  SER   442      41.694  17.203  38.282  1.00  0.00
ATOM    137  N   PHE   443      38.894  13.919  36.380  1.00  0.00
ATOM    138  CA  PHE   443      38.637  12.528  36.168  1.00  0.00
ATOM    139  C   PHE   443      37.734  12.256  34.952  1.00  0.00
ATOM    140  O   PHE   443      36.997  13.140  34.474  1.00  0.00
ATOM    141  CB  PHE   443      37.956  11.998  37.431  1.00  0.00
ATOM    142  CG  PHE   443      38.711  12.171  38.670  1.00  0.00
ATOM    143  CD1 PHE   443      38.758  13.422  39.280  1.00  0.00
ATOM    144  CD2 PHE   443      39.373  11.107  39.272  1.00  0.00
ATOM    145  CE1 PHE   443      39.453  13.606  40.476  1.00  0.00
ATOM    146  CE2 PHE   443      40.069  11.280  40.461  1.00  0.00
ATOM    147  CZ  PHE   443      40.109  12.533  41.066  1.00  0.00
ATOM    148  N   LYS   444      37.995  11.065  34.377  1.00  0.00
ATOM    149  CA  LYS   444      37.235  10.515  33.279  1.00  0.00
ATOM    150  C   LYS   444      36.008   9.776  33.922  1.00  0.00
ATOM    151  O   LYS   444      35.818   8.574  33.681  1.00  0.00
ATOM    152  CB  LYS   444      38.145   9.618  32.422  1.00  0.00
ATOM    153  CG  LYS   444      37.396   9.045  31.204  1.00  0.00
ATOM    154  CD  LYS   444      37.275  10.061  30.078  1.00  0.00
ATOM    155  CE  LYS   444      37.190   9.413  28.705  1.00  0.00
ATOM    156  NZ  LYS   444      36.548  10.239  27.691  1.00  0.00
ATOM    157  N   ASN   445      35.047  10.586  34.395  1.00  0.00
ATOM    158  CA  ASN   445      33.773  10.172  35.043  1.00  0.00
ATOM    159  C   ASN   445      32.980  11.474  35.339  1.00  0.00
ATOM    160  O   ASN   445      32.298  12.019  34.461  1.00  0.00
ATOM    161  CB  ASN   445      33.984   9.415  36.381  1.00  0.00
ATOM    162  CG  ASN   445      34.888   8.257  36.305  1.00  0.00
ATOM    163  OD1 ASN   445      34.689   7.257  35.625  1.00  0.00
ATOM    164  ND2 ASN   445      35.980   8.320  37.037  1.00  0.00
ATOM    165  OXT ASN   445      33.201  11.984  36.471  1.00  0.00
TER
END
