
#######################################################
#                                                     #
#                        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   17 (  137),  selected   17 , name T0349TS319_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   17 , name T0349_D1.pdb
# PARAMETERS: T0349TS319_5-D1.T0349_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:    17        23 - 54          3.22     3.22
  LCS_AVERAGE:     29.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        46 - 53          1.43     9.34
  LCS_AVERAGE:     11.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        49 - 53          0.92     9.61
  LCS_AVERAGE:      6.71

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:   57
LCS_GDT     A      23     A      23      3    6   17     3    4    5    6    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     D      24     D      24      4    6   17     3    3    5    5    8    9   11   13   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     I      25     I      25      4    6   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     G      26     G      26      4    6   17     3    3    4    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     H      27     H      27      4    6   17     3    3    5    6    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     L      28     L      28      3    6   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V      29     V      29      3    6   17     3    3    4    4    7   10   12   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     P      45     P      45      0    5   17     0    0    3    4    5    5    6    9   13   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     R      46     R      46      4    8   17     4    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     R      47     R      47      4    8   17     4    5    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V      48     V      48      4    8   17     4    5    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     L      49     L      49      5    8   17     4    4    6    6    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V      50     V      50      5    8   17     4    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     H      51     H      51      5    8   17     4    5    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     E      52     E      52      5    8   17     4    5    6    7    8   10   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     D      53     D      53      5    8   17     4    5    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     D      54     D      54      3    3   17     0    3    3    3    3    4    4    9   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  16.10  (   6.71   11.76   29.82 )

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      5      6      7      8     12     13     14     15     16     17     17     17     17     17     17     17     17     17     17 
GDT PERCENT_CA   7.02   8.77  10.53  12.28  14.04  21.05  22.81  24.56  26.32  28.07  29.82  29.82  29.82  29.82  29.82  29.82  29.82  29.82  29.82  29.82
GDT RMS_LOCAL    0.20   0.77   0.90   1.18   1.43   2.26   2.46   2.62   2.86   3.03   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.22
GDT RMS_ALL_CA   9.39   9.01   8.92   9.16   9.34   3.39   3.39   3.45   3.35   3.27   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.22

#      Molecule1      Molecule2       DISTANCE
LGA    A      23      A      23          2.734
LGA    D      24      D      24          6.341
LGA    I      25      I      25          3.879
LGA    G      26      G      26          3.590
LGA    H      27      H      27          3.544
LGA    L      28      L      28          1.528
LGA    V      29      V      29          3.932
LGA    P      45      P      45          4.741
LGA    R      46      R      46          1.685
LGA    R      47      R      47          2.697
LGA    V      48      V      48          1.940
LGA    L      49      L      49          2.629
LGA    V      50      V      50          1.272
LGA    H      51      H      51          3.412
LGA    E      52      E      52          3.659
LGA    D      53      D      53          2.157
LGA    D      54      D      54          4.931

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17   57    4.0     14    2.62    18.860    18.477     0.516

LGA_LOCAL      RMSD =  2.615  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.471  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  3.224  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.389340 * X  +   0.031385 * Y  +   0.920559 * Z  +  -0.991812
  Y_new =  -0.818864 * X  +   0.469412 * Y  +   0.330325 * Z  +  10.583065
  Z_new =  -0.421754 * X  +  -0.882421 * Y  +   0.208461 * Z  +   1.503520 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.338812    1.802781  [ DEG:   -76.7083    103.2917 ]
  Theta =   0.435379    2.706214  [ DEG:    24.9454    155.0546 ]
  Phi   =  -1.126969    2.014623  [ DEG:   -64.5706    115.4294 ]
 
# 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: T0349TS319_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS319_5-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17   57   4.0   14   2.62  18.477     3.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS319_5-D1
PFRMAT TS
TARGET T0349
MODEL 5
PARENT N/A
ATOM      1  N   ALA    23      -2.225  12.928   8.244  1.00 12.98       1SG   2
ATOM      2  CA  ALA    23      -1.231  13.974   7.920  1.00 12.98       1SG   3
ATOM      3  CB  ALA    23       0.119  13.666   8.586  1.00 12.98       1SG   4
ATOM      4  C   ALA    23      -1.014  14.088   6.450  1.00 12.98       1SG   5
ATOM      5  O   ALA    23      -1.961  14.164   5.670  1.00 12.98       1SG   6
ATOM      6  N   ASP    24       0.269  14.127   6.044  1.00 48.31       1SG   7
ATOM      7  CA  ASP    24       0.626  14.292   4.667  1.00 48.31       1SG   8
ATOM      8  CB  ASP    24       2.140  14.495   4.459  1.00 48.31       1SG   9
ATOM      9  CG  ASP    24       2.519  15.853   5.030  1.00 48.31       1SG  10
ATOM     10  OD1 ASP    24       1.684  16.435   5.771  1.00 48.31       1SG  11
ATOM     11  OD2 ASP    24       3.647  16.328   4.727  1.00 48.31       1SG  12
ATOM     12  C   ASP    24       0.231  13.094   3.856  1.00 48.31       1SG  13
ATOM     13  O   ASP    24      -0.288  13.236   2.752  1.00 48.31       1SG  14
ATOM     14  N   ILE    25       0.434  11.878   4.398  1.00157.26       1SG  15
ATOM     15  CA  ILE    25       0.258  10.670   3.639  1.00157.26       1SG  16
ATOM     16  CB  ILE    25       0.884   9.473   4.311  1.00157.26       1SG  17
ATOM     17  CG2 ILE    25      -0.041   9.071   5.473  1.00157.26       1SG  18
ATOM     18  CG1 ILE    25       1.184   8.313   3.340  1.00157.26       1SG  19
ATOM     19  CD1 ILE    25      -0.037   7.606   2.760  1.00157.26       1SG  20
ATOM     20  C   ILE    25      -1.196  10.390   3.420  1.00157.26       1SG  21
ATOM     21  O   ILE    25      -2.029  10.621   4.296  1.00157.26       1SG  22
ATOM     22  N   GLY    26      -1.529   9.923   2.195  1.00 35.79       1SG  23
ATOM     23  CA  GLY    26      -2.866   9.526   1.849  1.00 35.79       1SG  24
ATOM     24  C   GLY    26      -2.793   8.112   1.356  1.00 35.79       1SG  25
ATOM     25  O   GLY    26      -1.871   7.728   0.638  1.00 35.79       1SG  26
ATOM     26  N   HIS    27      -3.807   7.303   1.713  1.00107.43       1SG  27
ATOM     27  CA  HIS    27      -3.824   5.906   1.392  1.00107.43       1SG  28
ATOM     28  ND1 HIS    27      -3.859   6.613   4.550  1.00107.43       1SG  29
ATOM     29  CG  HIS    27      -3.720   5.420   3.869  1.00107.43       1SG  30
ATOM     30  CB  HIS    27      -4.415   5.117   2.571  1.00107.43       1SG  31
ATOM     31  NE2 HIS    27      -2.461   5.362   5.745  1.00107.43       1SG  32
ATOM     32  CD2 HIS    27      -2.864   4.669   4.619  1.00107.43       1SG  33
ATOM     33  CE1 HIS    27      -3.083   6.524   5.663  1.00107.43       1SG  34
ATOM     34  C   HIS    27      -4.755   5.736   0.234  1.00107.43       1SG  35
ATOM     35  O   HIS    27      -5.965   5.638   0.427  1.00107.43       1SG  36
ATOM     36  N   LEU    28      -4.233   5.691  -1.011  1.00101.48       1SG  37
ATOM     37  CA  LEU    28      -5.173   5.544  -2.086  1.00101.48       1SG  38
ATOM     38  CB  LEU    28      -5.533   6.847  -2.828  1.00101.48       1SG  39
ATOM     39  CG  LEU    28      -6.121   7.954  -1.929  1.00101.48       1SG  40
ATOM     40  CD2 LEU    28      -6.995   8.931  -2.732  1.00101.48       1SG  41
ATOM     41  CD1 LEU    28      -5.036   8.649  -1.086  1.00101.48       1SG  42
ATOM     42  C   LEU    28      -4.640   4.607  -3.119  1.00101.48       1SG  43
ATOM     43  O   LEU    28      -3.445   4.322  -3.187  1.00101.48       1SG  44
ATOM     44  N   VAL    29      -5.571   4.069  -3.925  1.00 42.05       1SG  45
ATOM     45  CA  VAL    29      -5.290   3.184  -5.016  1.00 42.05       1SG  46
ATOM     46  CB  VAL    29      -6.560   2.679  -5.630  1.00 42.05       1SG  47
ATOM     47  CG1 VAL    29      -6.227   1.849  -6.881  1.00 42.05       1SG  48
ATOM     48  CG2 VAL    29      -7.346   1.925  -4.544  1.00 42.05       1SG  49
ATOM     49  C   VAL    29      -4.554   3.942  -6.078  1.00 42.05       1SG  50
ATOM     50  O   VAL    29      -3.561   3.466  -6.625  1.00 42.05       1SG  51
ATOM    160  N   PRO    45      -0.322  -4.881  -0.182  1.00183.50       1SG 161
ATOM    161  CA  PRO    45      -0.287  -3.610  -0.856  1.00183.50       1SG 162
ATOM    162  CD  PRO    45       1.046  -5.159   0.261  1.00183.50       1SG 163
ATOM    163  CB  PRO    45       1.034  -2.919  -0.514  1.00183.50       1SG 164
ATOM    164  CG  PRO    45       1.976  -4.093  -0.319  1.00183.50       1SG 165
ATOM    165  C   PRO    45      -0.497  -3.545  -2.307  1.00183.50       1SG 166
ATOM    166  O   PRO    45       0.444  -3.368  -3.071  1.00183.50       1SG 167
ATOM    167  N   ARG    46      -1.777  -3.696  -2.666  1.00184.08       1SG 168
ATOM    168  CA  ARG    46      -2.247  -3.404  -3.970  1.00184.08       1SG 169
ATOM    169  CB  ARG    46      -3.610  -4.052  -4.270  1.00184.08       1SG 170
ATOM    170  CG  ARG    46      -3.924  -4.140  -5.765  1.00184.08       1SG 171
ATOM    171  CD  ARG    46      -5.248  -4.833  -6.093  1.00184.08       1SG 172
ATOM    172  NE  ARG    46      -6.310  -4.059  -5.398  1.00184.08       1SG 173
ATOM    173  CZ  ARG    46      -6.753  -2.890  -5.943  1.00184.08       1SG 174
ATOM    174  NH1 ARG    46      -6.272  -2.477  -7.153  1.00184.08       1SG 175
ATOM    175  NH2 ARG    46      -7.659  -2.129  -5.264  1.00184.08       1SG 176
ATOM    176  C   ARG    46      -2.363  -1.912  -3.947  1.00184.08       1SG 177
ATOM    177  O   ARG    46      -2.211  -1.230  -4.960  1.00184.08       1SG 178
ATOM    178  N   ARG    47      -2.643  -1.393  -2.729  1.00129.96       1SG 179
ATOM    179  CA  ARG    47      -2.852  -0.001  -2.450  1.00129.96       1SG 180
ATOM    180  CB  ARG    47      -3.584   0.259  -1.118  1.00129.96       1SG 181
ATOM    181  CG  ARG    47      -5.025  -0.252  -1.105  1.00129.96       1SG 182
ATOM    182  CD  ARG    47      -5.774   0.018  -2.413  1.00129.96       1SG 183
ATOM    183  NE  ARG    47      -7.194  -0.400  -2.228  1.00129.96       1SG 184
ATOM    184  CZ  ARG    47      -8.105   0.484  -1.724  1.00129.96       1SG 185
ATOM    185  NH1 ARG    47      -7.719   1.755  -1.409  1.00129.96       1SG 186
ATOM    186  NH2 ARG    47      -9.402   0.106  -1.530  1.00129.96       1SG 187
ATOM    187  C   ARG    47      -1.536   0.702  -2.377  1.00129.96       1SG 188
ATOM    188  O   ARG    47      -0.501   0.091  -2.116  1.00129.96       1SG 189
ATOM    189  N   VAL    48      -1.549   2.028  -2.625  1.00 42.53       1SG 190
ATOM    190  CA  VAL    48      -0.338   2.791  -2.615  1.00 42.53       1SG 191
ATOM    191  CB  VAL    48      -0.106   3.557  -3.888  1.00 42.53       1SG 192
ATOM    192  CG1 VAL    48       1.097   4.494  -3.689  1.00 42.53       1SG 193
ATOM    193  CG2 VAL    48       0.074   2.562  -5.042  1.00 42.53       1SG 194
ATOM    194  C   VAL    48      -0.422   3.830  -1.549  1.00 42.53       1SG 195
ATOM    195  O   VAL    48      -1.482   4.402  -1.294  1.00 42.53       1SG 196
ATOM    196  N   LEU    49       0.719   4.088  -0.883  1.00 65.67       1SG 197
ATOM    197  CA  LEU    49       0.775   5.162   0.056  1.00 65.67       1SG 198
ATOM    198  CB  LEU    49       1.892   5.025   1.108  1.00 65.67       1SG 199
ATOM    199  CG  LEU    49       1.659   3.966   2.199  1.00 65.67       1SG 200
ATOM    200  CD2 LEU    49       0.391   4.278   3.008  1.00 65.67       1SG 201
ATOM    201  CD1 LEU    49       2.888   3.850   3.118  1.00 65.67       1SG 202
ATOM    202  C   LEU    49       1.151   6.335  -0.773  1.00 65.67       1SG 203
ATOM    203  O   LEU    49       2.315   6.494  -1.149  1.00 65.67       1SG 204
ATOM    204  N   VAL    50       0.174   7.196  -1.090  1.00 44.15       1SG 205
ATOM    205  CA  VAL    50       0.505   8.302  -1.930  1.00 44.15       1SG 206
ATOM    206  CB  VAL    50      -0.587   8.700  -2.872  1.00 44.15       1SG 207
ATOM    207  CG1 VAL    50      -0.158   9.983  -3.603  1.00 44.15       1SG 208
ATOM    208  CG2 VAL    50      -0.865   7.522  -3.820  1.00 44.15       1SG 209
ATOM    209  C   VAL    50       0.775   9.457  -1.037  1.00 44.15       1SG 210
ATOM    210  O   VAL    50       0.004   9.742  -0.123  1.00 44.15       1SG 211
ATOM    211  N   HIS    51       1.894  10.156  -1.296  1.00102.56       1SG 212
ATOM    212  CA  HIS    51       2.268  11.247  -0.450  1.00102.56       1SG 213
ATOM    213  ND1 HIS    51       4.881  13.235   0.861  1.00102.56       1SG 214
ATOM    214  CG  HIS    51       4.132  12.097   1.062  1.00102.56       1SG 215
ATOM    215  CB  HIS    51       3.743  11.147  -0.026  1.00102.56       1SG 216
ATOM    216  NE2 HIS    51       4.429  13.147   3.036  1.00102.56       1SG 217
ATOM    217  CD2 HIS    51       3.862  12.059   2.393  1.00102.56       1SG 218
ATOM    218  CE1 HIS    51       5.029  13.823   2.072  1.00102.56       1SG 219
ATOM    219  C   HIS    51       2.059  12.522  -1.199  1.00102.56       1SG 220
ATOM    220  O   HIS    51       2.445  12.656  -2.361  1.00102.56       1SG 221
ATOM    221  N   GLU    52       1.422  13.506  -0.535  1.00 84.46       1SG 222
ATOM    222  CA  GLU    52       1.161  14.766  -1.161  1.00 84.46       1SG 223
ATOM    223  CB  GLU    52       0.393  15.727  -0.243  1.00 84.46       1SG 224
ATOM    224  CG  GLU    52      -0.182  16.967  -0.926  1.00 84.46       1SG 225
ATOM    225  CD  GLU    52      -1.204  17.534   0.044  1.00 84.46       1SG 226
ATOM    226  OE1 GLU    52      -2.074  16.744   0.495  1.00 84.46       1SG 227
ATOM    227  OE2 GLU    52      -1.125  18.753   0.360  1.00 84.46       1SG 228
ATOM    228  C   GLU    52       2.502  15.332  -1.461  1.00 84.46       1SG 229
ATOM    229  O   GLU    52       3.424  15.208  -0.660  1.00 84.46       1SG 230
ATOM    230  N   ASP    53       2.663  15.952  -2.641  1.00 44.76       1SG 231
ATOM    231  CA  ASP    53       3.976  16.416  -2.948  1.00 44.76       1SG 232
ATOM    232  CB  ASP    53       4.154  16.836  -4.418  1.00 44.76       1SG 233
ATOM    233  CG  ASP    53       4.119  15.562  -5.254  1.00 44.76       1SG 234
ATOM    234  OD1 ASP    53       4.535  14.498  -4.721  1.00 44.76       1SG 235
ATOM    235  OD2 ASP    53       3.672  15.631  -6.431  1.00 44.76       1SG 236
ATOM    236  C   ASP    53       4.278  17.560  -2.046  1.00 44.76       1SG 237
ATOM    237  O   ASP    53       3.394  18.310  -1.640  1.00 44.76       1SG 238
ATOM    238  N   ASP    54       5.566  17.700  -1.690  1.00 24.27       1SG 239
ATOM    239  CA  ASP    54       5.948  18.759  -0.806  1.00 24.27       1SG 240
ATOM    240  CB  ASP    54       5.606  20.152  -1.347  1.00 24.27       1SG 241
ATOM    241  CG  ASP    54       6.502  20.403  -2.546  1.00 24.27       1SG 242
ATOM    242  OD1 ASP    54       7.414  19.565  -2.788  1.00 24.27       1SG 243
ATOM    243  OD2 ASP    54       6.282  21.429  -3.239  1.00 24.27       1SG 244
ATOM    244  C   ASP    54       5.194  18.569   0.499  1.00 24.27       1SG 245
ATOM    245  O   ASP    54       4.735  17.425   0.762  1.00 24.27       1SG 246
ATOM    246  OXT ASP    54       5.069  19.568   1.256  1.00 24.27       1SG 247
TER
END
