
#######################################################
#                                                     #
#                        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   16 (  121),  selected   16 , name T0335TS389_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   16 , name T0335_D1.pdb
# PARAMETERS: T0335TS389_3-D1.T0335_D1.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:    10         9 - 27          4.52     9.63
  LCS_AVERAGE:     22.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        20 - 27          1.96    12.93
  LCS_AVERAGE:     17.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        21 - 27          0.75    13.68
  LCS_AVERAGE:     15.28

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:   36
LCS_GDT     A       5     A       5      6    6    7     4    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     K       6     K       6      6    6    7     5    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     I       7     I       7      6    6    7     5    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     A       8     A       8      6    6    7     5    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     R       9     R       9      6    6   10     5    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     I      10     I      10      6    6   10     5    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     G      20     G      20      3    8   10     0    3    4    4    5    6    7    8    8    8    8    8    9   10   12   13   14   14   14   14 
LCS_GDT     V      21     V      21      7    8   10     3    4    7    7    7    7    7    8    8    8    8    8    9    9   12   13   14   14   14   14 
LCS_GDT     I      22     I      22      7    8   10     5    6    7    7    7    7    7    8    8    9   10   12   12   12   12   13   14   14   14   14 
LCS_GDT     T      23     T      23      7    8   10     5    6    7    7    7    7    7    8   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     E      24     E      24      7    8   10     5    6    7    7    7    7    7    8   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     E      25     E      25      7    8   10     5    6    7    7    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     E      26     E      26      7    8   10     5    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     K      27     K      27      7    8   10     4    6    8    8    9    9    9    9   11   11   11   12   12   12   12   13   14   14   14   14 
LCS_GDT     K      39     K      39      0    0    0     0    0    0    0    0    0    0    0    0    4    4    4    4    4    4    4    5    5    5   11 
LCS_GDT     G      40     G      40      0    0    0     0    0    0    0    0    0    0    2    3    4    4    4    4    4    4    4    5    5    5    7 
LCS_AVERAGE  LCS_A:  18.29  (  15.28   17.36   22.22 )

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      6      8      8      9      9      9      9     11     11     11     12     12     12     12     13     14     14     14     14 
GDT PERCENT_CA  13.89  16.67  22.22  22.22  25.00  25.00  25.00  25.00  30.56  30.56  30.56  33.33  33.33  33.33  33.33  36.11  38.89  38.89  38.89  38.89
GDT RMS_LOCAL    0.20   0.46   1.07   1.07   1.83   1.83   1.83   1.83   2.98   2.98   2.98   3.66   3.66   3.66   3.66   4.56   5.23   5.23   5.23   5.23
GDT RMS_ALL_CA  13.88  14.19   9.89   9.89   9.50   9.50   9.50   9.50   9.08   9.08   9.08   9.17   9.17   9.17   9.17   9.22   9.22   9.22   9.22   9.22

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.236
LGA    K       6      K       6          1.064
LGA    I       7      I       7          1.157
LGA    A       8      A       8          2.970
LGA    R       9      R       9          2.123
LGA    I      10      I      10          2.506
LGA    G      20      G      20         12.036
LGA    V      21      V      21         11.868
LGA    I      22      I      22          8.470
LGA    T      23      T      23          5.287
LGA    E      24      E      24          4.748
LGA    E      25      E      25          2.657
LGA    E      26      E      26          2.448
LGA    K      27      K      27          2.650
LGA    K      39      K      39         19.020
LGA    G      40      G      40         22.435

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   36    4.0      9    1.83    25.000    24.272     0.467

LGA_LOCAL      RMSD =  1.828  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.084  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  8.055  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.618158 * X  +  -0.552998 * Y  +  -0.558635 * Z  +  13.440468
  Y_new =  -0.315455 * X  +  -0.476419 * Y  +   0.820678 * Z  +  -2.198662
  Z_new =  -0.719978 * X  +   0.683533 * Y  +   0.120057 * Z  +   1.895682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.396929   -1.744664  [ DEG:    80.0381    -99.9619 ]
  Theta =   0.803771    2.337821  [ DEG:    46.0527    133.9473 ]
  Phi   =  -2.669728    0.471865  [ DEG:  -152.9642     27.0358 ]
 
# 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: T0335TS389_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS389_3-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   36   4.0    9   1.83  24.272     8.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS389_3-D1
PFRMAT TS
TARGET T0335
MODEL  3
PARENT N/A
ATOM     16  N   ALA     5      -3.309  -9.561  -6.626  1.00  0.00
ATOM     17  CA  ALA     5      -2.960  -9.968  -5.235  1.00  0.00
ATOM     18  CB  ALA     5      -2.265 -11.321  -5.238  1.00  0.00
ATOM     19  O   ALA     5      -2.311  -8.371  -3.569  1.00  0.00
ATOM     20  C   ALA     5      -2.021  -8.936  -4.602  1.00  0.00
ATOM     21  N   LYS     6      -0.896  -8.692  -5.217  1.00  0.00
ATOM     22  CA  LYS     6       0.063  -7.699  -4.651  1.00  0.00
ATOM     23  CB  LYS     6       1.310  -7.596  -5.531  1.00  0.00
ATOM     24  CG  LYS     6       2.363  -6.634  -5.006  1.00  0.00
ATOM     25  CD  LYS     6       3.601  -6.635  -5.889  1.00  0.00
ATOM     26  CE  LYS     6       4.634  -5.636  -5.392  1.00  0.00
ATOM     27  NZ  LYS     6       5.843  -5.608  -6.262  1.00  0.00
ATOM     28  O   LYS     6      -0.499  -5.635  -3.569  1.00  0.00
ATOM     29  C   LYS     6      -0.593  -6.319  -4.569  1.00  0.00
ATOM     30  N   ILE     7      -1.259  -5.903  -5.613  1.00  0.00
ATOM     31  CA  ILE     7      -1.921  -4.568  -5.584  1.00  0.00
ATOM     32  CB  ILE     7      -2.929  -4.413  -6.737  1.00  0.00
ATOM     33  CG1 ILE     7      -2.198  -4.356  -8.080  1.00  0.00
ATOM     34  CG2 ILE     7      -3.735  -3.133  -6.573  1.00  0.00
ATOM     35  CD1 ILE     7      -3.114  -4.474  -9.280  1.00  0.00
ATOM     36  O   ILE     7      -2.681  -3.324  -3.679  1.00  0.00
ATOM     37  C   ILE     7      -2.673  -4.391  -4.263  1.00  0.00
ATOM     38  N   ALA     8      -3.301  -5.430  -3.786  1.00  0.00
ATOM     39  CA  ALA     8      -4.048  -5.326  -2.500  1.00  0.00
ATOM     40  CB  ALA     8      -5.055  -6.459  -2.379  1.00  0.00
ATOM     41  O   ALA     8      -3.343  -4.913  -0.246  1.00  0.00
ATOM     42  C   ALA     8      -3.073  -5.405  -1.323  1.00  0.00
ATOM     43  N   ARG     9      -1.939  -6.019  -1.523  1.00  0.00
ATOM     44  CA  ARG     9      -0.944  -6.131  -0.419  1.00  0.00
ATOM     45  CB  ARG     9       0.224  -7.026  -0.838  1.00  0.00
ATOM     46  CG  ARG     9      -0.132  -8.498  -0.953  1.00  0.00
ATOM     47  CD  ARG     9       1.050  -9.314  -1.453  1.00  0.00
ATOM     48  NE  ARG     9       0.721 -10.732  -1.578  1.00  0.00
ATOM     49  CZ  ARG     9       1.529 -11.642  -2.114  1.00  0.00
ATOM     50  NH1 ARG     9       1.147 -12.909  -2.185  1.00  0.00
ATOM     51  NH2 ARG     9       2.718 -11.281  -2.576  1.00  0.00
ATOM     52  O   ARG     9      -0.110  -4.456   1.081  1.00  0.00
ATOM     53  C   ARG     9      -0.399  -4.746  -0.063  1.00  0.00
ATOM     54  N   ILE    10      -0.258  -3.886  -1.035  1.00  0.00
ATOM     55  CA  ILE    10       0.265  -2.518  -0.750  1.00  0.00
ATOM     56  CB  ILE    10       0.717  -1.807  -2.039  1.00  0.00
ATOM     57  CG1 ILE    10       1.937  -2.511  -2.636  1.00  0.00
ATOM     58  CG2 ILE    10       1.092  -0.361  -1.745  1.00  0.00
ATOM     59  CD1 ILE    10       2.296  -2.034  -4.026  1.00  0.00
ATOM     60  O   ILE    10      -0.545  -0.777   0.686  1.00  0.00
ATOM     61  C   ILE    10      -0.824  -1.670  -0.092  1.00  0.00
ATOM     62  N   GLY    20      -2.062  -1.940  -0.398  1.00  0.00
ATOM     63  CA  GLY    20      -3.170  -1.151   0.210  1.00  0.00
ATOM     64  O   GLY    20      -3.841  -0.963   2.505  1.00  0.00
ATOM     65  C   GLY    20      -3.501  -1.700   1.600  1.00  0.00
ATOM     66  N   VAL    21      -3.401  -2.989   1.775  1.00  0.00
ATOM     67  CA  VAL    21      -3.708  -3.589   3.104  1.00  0.00
ATOM     68  CB  VAL    21      -3.429  -5.103   3.118  1.00  0.00
ATOM     69  CG1 VAL    21      -3.558  -5.656   4.529  1.00  0.00
ATOM     70  CG2 VAL    21      -4.415  -5.836   2.222  1.00  0.00
ATOM     71  O   VAL    21      -3.222  -2.880   5.343  1.00  0.00
ATOM     72  C   VAL    21      -2.847  -2.936   4.188  1.00  0.00
ATOM     73  N   ILE    22      -1.694  -2.444   3.825  1.00  0.00
ATOM     74  CA  ILE    22      -0.809  -1.796   4.837  1.00  0.00
ATOM     75  CB  ILE    22       0.299  -0.963   4.167  1.00  0.00
ATOM     76  CG1 ILE    22      -0.313   0.161   3.327  1.00  0.00
ATOM     77  CG2 ILE    22       1.145  -1.838   3.256  1.00  0.00
ATOM     78  CD1 ILE    22       0.703   1.150   2.801  1.00  0.00
ATOM     79  O   ILE    22      -2.682  -0.389   5.350  1.00  0.00
ATOM     80  C   ILE    22      -1.631  -0.865   5.732  1.00  0.00
ATOM     81  N   THR    23      -1.161  -0.602   6.921  1.00  0.00
ATOM     82  CA  THR    23      -1.918   0.297   7.838  1.00  0.00
ATOM     83  CB  THR    23      -1.575   0.017   9.313  1.00  0.00
ATOM     84  CG2 THR    23      -1.865  -1.435   9.661  1.00  0.00
ATOM     85  OG1 THR    23      -0.186   0.281   9.542  1.00  0.00
ATOM     86  O   THR    23      -0.551   2.068   6.973  1.00  0.00
ATOM     87  C   THR    23      -1.580   1.761   7.542  1.00  0.00
ATOM     88  N   GLU    24      -2.438   2.667   7.925  1.00  0.00
ATOM     89  CA  GLU    24      -2.163   4.109   7.669  1.00  0.00
ATOM     90  CB  GLU    24      -3.331   4.971   8.153  1.00  0.00
ATOM     91  CG  GLU    24      -4.589   4.842   7.308  1.00  0.00
ATOM     92  CD  GLU    24      -5.751   5.637   7.870  1.00  0.00
ATOM     93  OE1 GLU    24      -5.593   6.231   8.958  1.00  0.00
ATOM     94  OE2 GLU    24      -6.819   5.666   7.223  1.00  0.00
ATOM     95  O   GLU    24      -0.204   5.454   7.999  1.00  0.00
ATOM     96  C   GLU    24      -0.894   4.542   8.409  1.00  0.00
ATOM     97  N   GLU    25      -0.582   3.892   9.498  1.00  0.00
ATOM     98  CA  GLU    25       0.641   4.267  10.262  1.00  0.00
ATOM     99  CB  GLU    25       0.564   3.727  11.692  1.00  0.00
ATOM    100  CG  GLU    25      -0.534   4.359  12.536  1.00  0.00
ATOM    101  CD  GLU    25      -0.594   3.786  13.937  1.00  0.00
ATOM    102  OE1 GLU    25       0.254   2.931  14.266  1.00  0.00
ATOM    103  OE2 GLU    25      -1.490   4.191  14.707  1.00  0.00
ATOM    104  O   GLU    25       2.988   4.152   9.787  1.00  0.00
ATOM    105  C   GLU    25       1.886   3.683   9.589  1.00  0.00
ATOM    106  N   GLU    26       1.716   2.665   8.791  1.00  0.00
ATOM    107  CA  GLU    26       2.888   2.050   8.103  1.00  0.00
ATOM    108  CB  GLU    26       2.485   0.739   7.425  1.00  0.00
ATOM    109  CG  GLU    26       3.636   0.012   6.749  1.00  0.00
ATOM    110  CD  GLU    26       3.206  -1.298   6.118  1.00  0.00
ATOM    111  OE1 GLU    26       2.007  -1.636   6.207  1.00  0.00
ATOM    112  OE2 GLU    26       4.069  -1.988   5.534  1.00  0.00
ATOM    113  O   GLU    26       4.620   3.260   6.967  1.00  0.00
ATOM    114  C   GLU    26       3.435   3.001   7.036  1.00  0.00
ATOM    115  N   LYS    27       2.577   3.530   6.204  1.00  0.00
ATOM    116  CA  LYS    27       3.048   4.465   5.142  1.00  0.00
ATOM    117  CB  LYS    27       1.984   4.619   4.053  1.00  0.00
ATOM    118  CG  LYS    27       1.680   3.337   3.297  1.00  0.00
ATOM    119  CD  LYS    27       2.877   2.884   2.475  1.00  0.00
ATOM    120  CE  LYS    27       2.536   1.671   1.623  1.00  0.00
ATOM    121  NZ  LYS    27       3.700   1.215   0.817  1.00  0.00
ATOM    122  O   LYS    27       4.058   6.640   5.185  1.00  0.00
ATOM    123  C   LYS    27       3.334   5.842   5.747  1.00  0.00
ATOM    124  N   LYS    39       2.773   6.124   6.889  1.00  0.00
ATOM    125  CA  LYS    39       3.014   7.448   7.532  1.00  0.00
ATOM    126  CB  LYS    39       2.075   7.644   8.724  1.00  0.00
ATOM    127  CG  LYS    39       2.217   8.992   9.412  1.00  0.00
ATOM    128  CD  LYS    39       1.198   9.152  10.528  1.00  0.00
ATOM    129  CE  LYS    39       1.362  10.487  11.239  1.00  0.00
ATOM    130  NZ  LYS    39       0.407  10.636  12.370  1.00  0.00
ATOM    131  O   LYS    39       5.147   8.510   7.794  1.00  0.00
ATOM    132  C   LYS    39       4.458   7.537   8.031  1.00  0.00
ATOM    133  N   GLY    40       4.922   6.530   8.720  1.00  0.00
ATOM    134  CA  GLY    40       6.322   6.558   9.232  1.00  0.00
ATOM    135  O   GLY    40       8.345   6.912   7.993  1.00  0.00
ATOM    136  C   GLY    40       7.308   6.287   8.093  1.00  0.00
TER
END
