
#######################################################
#                                                     #
#                        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   14 (  115),  selected   14 , name T0319TS468_1
# Molecule2: number of CA atoms  135 ( 1055),  selected   14 , name T0319.pdb
# PARAMETERS: T0319TS468_1.T0319.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:    14       108 - 121         0.57     0.57
  LCS_AVERAGE:     10.37

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       108 - 121         0.57     0.57
  LCS_AVERAGE:     10.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       108 - 121         0.57     0.57
  LCS_AVERAGE:     10.37

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:  135
LCS_GDT     G     108     G     108     14   14   14     9   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     109     E     109     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     M     110     M     110     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     K     111     K     111     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     C     112     C     112     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     R     113     R     113     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     114     N     114     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     C     115     C     115     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     G     116     G     116     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     H     117     H     117     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     I     118     I     118     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     Y     119     Y     119     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     Y     120     Y     120     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     I     121     I     121     14   14   14     3    3   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:  10.37  (  10.37   10.37   10.37 )

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     11     13     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   8.15   9.63  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37  10.37
GDT RMS_LOCAL    0.28   0.39   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57
GDT RMS_ALL_CA   0.75   0.61   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57

#      Molecule1      Molecule2       DISTANCE
LGA    G     108      G     108          0.451
LGA    E     109      E     109          0.576
LGA    M     110      M     110          0.433
LGA    K     111      K     111          0.594
LGA    C     112      C     112          0.479
LGA    R     113      R     113          0.467
LGA    N     114      N     114          0.568
LGA    C     115      C     115          0.279
LGA    G     116      G     116          0.143
LGA    H     117      H     117          0.217
LGA    I     118      I     118          0.317
LGA    Y     119      Y     119          0.592
LGA    Y     120      Y     120          0.311
LGA    I     121      I     121          1.428

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  135    4.0     14    0.57    10.185    10.312     2.084

LGA_LOCAL      RMSD =  0.572  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.572  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  0.572  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.309331 * X  +   0.912090 * Y  +   0.269084 * Z  +  -9.005777
  Y_new =   0.552692 * X  +   0.057829 * Y  +  -0.831377 * Z  +  11.303617
  Z_new =  -0.773851 * X  +   0.405891 * Y  +  -0.486216 * Z  +  24.816833 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.445992   -0.695601  [ DEG:   140.1450    -39.8550 ]
  Theta =   0.884900    2.256693  [ DEG:    50.7010    129.2990 ]
  Phi   =   1.060550   -2.081042  [ DEG:    60.7651   -119.2349 ]
 
# 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: T0319TS468_1                                  
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319TS468_1.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  135   4.0   14   0.57  10.312     0.57
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS468_1
PFRMAT TS
TARGET T0319    
MODEL  1
PARENT n/a
ATOM      1  N   GLY   108      16.181  13.536   9.865  1.00  0.00
ATOM      2  CA  GLY   108      15.609  12.692  10.905  1.00  0.00
ATOM      3  C   GLY   108      14.180  12.253  10.635  1.00  0.00
ATOM      4  O   GLY   108      13.594  11.522  11.431  1.00  0.00
ATOM      5  N   GLU   109      13.616  12.674   9.502  1.00  0.00
ATOM      6  CA  GLU   109      12.248  12.300   9.162  1.00  0.00
ATOM      7  C   GLU   109      12.182  10.823   8.800  1.00  0.00
ATOM      8  O   GLU   109      13.073  10.332   8.113  1.00  0.00
ATOM      9  CB  GLU   109      11.750  13.117   7.968  1.00  0.00
ATOM     10  CG  GLU   109      10.299  12.856   7.600  1.00  0.00
ATOM     11  CD  GLU   109       9.825  13.723   6.450  1.00  0.00
ATOM     12  OE1 GLU   109      10.636  14.519   5.932  1.00  0.00
ATOM     13  OE2 GLU   109       8.642  13.606   6.065  1.00  0.00
ATOM     14  N   MET   110      11.169  10.119   9.315  1.00  0.00
ATOM     15  CA  MET   110      10.933   8.699   8.990  1.00  0.00
ATOM     16  C   MET   110       9.450   8.574   8.629  1.00  0.00
ATOM     17  O   MET   110       8.596   9.158   9.293  1.00  0.00
ATOM     18  CB  MET   110      11.267   7.812  10.190  1.00  0.00
ATOM     19  CG  MET   110      10.991   6.334   9.965  1.00  0.00
ATOM     20  SD  MET   110      11.540   5.305  11.340  1.00  0.00
ATOM     21  CE  MET   110      10.334   5.739  12.591  1.00  0.00
ATOM     22  N   LYS   111       9.151   7.843   7.561  1.00  0.00
ATOM     23  CA  LYS   111       7.769   7.707   7.095  1.00  0.00
ATOM     24  C   LYS   111       7.367   6.238   7.086  1.00  0.00
ATOM     25  O   LYS   111       8.206   5.381   6.834  1.00  0.00
ATOM     26  CB  LYS   111       7.624   8.265   5.679  1.00  0.00
ATOM     27  CG  LYS   111       7.852   9.766   5.576  1.00  0.00
ATOM     28  CD  LYS   111       7.645  10.259   4.153  1.00  0.00
ATOM     29  CE  LYS   111       7.847  11.763   4.057  1.00  0.00
ATOM     30  NZ  LYS   111       7.619  12.266   2.673  1.00  0.00
ATOM     31  N   CYS   112       6.096   5.950   7.380  1.00  0.00
ATOM     32  CA  CYS   112       5.623   4.566   7.375  1.00  0.00
ATOM     33  C   CYS   112       5.401   4.087   5.925  1.00  0.00
ATOM     34  O   CYS   112       4.683   4.727   5.142  1.00  0.00
ATOM     35  CB  CYS   112       4.302   4.449   8.137  1.00  0.00
ATOM     36  SG  CYS   112       3.610   2.778   8.179  1.00  0.00
ATOM     37  N   ARG   113       6.034   2.966   5.576  1.00  0.00
ATOM     38  CA  ARG   113       5.903   2.428   4.224  1.00  0.00
ATOM     39  C   ARG   113       4.487   1.928   3.948  1.00  0.00
ATOM     40  O   ARG   113       4.045   1.905   2.803  1.00  0.00
ATOM     41  CB  ARG   113       6.861   1.253   4.020  1.00  0.00
ATOM     42  CG  ARG   113       8.326   1.650   3.959  1.00  0.00
ATOM     43  CD  ARG   113       9.222   0.432   3.804  1.00  0.00
ATOM     44  NE  ARG   113      10.638   0.791   3.805  1.00  0.00
ATOM     45  CZ  ARG   113      11.632  -0.087   3.901  1.00  0.00
ATOM     46  NH1 ARG   113      12.890   0.332   3.894  1.00  0.00
ATOM     47  NH2 ARG   113      11.365  -1.381   4.003  1.00  0.00
ATOM     48  N   ASN   114       3.769   1.573   5.011  1.00  0.00
ATOM     49  CA  ASN   114       2.405   1.078   4.874  1.00  0.00
ATOM     50  C   ASN   114       1.320   2.123   4.787  1.00  0.00
ATOM     51  O   ASN   114       0.534   2.113   3.849  1.00  0.00
ATOM     52  CB  ASN   114       2.030   0.203   6.072  1.00  0.00
ATOM     53  CG  ASN   114       2.776  -1.115   6.087  1.00  0.00
ATOM     54  OD1 ASN   114       3.308  -1.550   5.066  1.00  0.00
ATOM     55  ND2 ASN   114       2.819  -1.756   7.250  1.00  0.00
ATOM     56  N   CYS   115       1.262   3.015   5.781  1.00  0.00
ATOM     57  CA  CYS   115       0.198   4.017   5.837  1.00  0.00
ATOM     58  C   CYS   115       0.619   5.461   5.578  1.00  0.00
ATOM     59  O   CYS   115      -0.230   6.369   5.581  1.00  0.00
ATOM     60  CB  CYS   115      -0.456   4.026   7.220  1.00  0.00
ATOM     61  SG  CYS   115      -1.218   2.457   7.697  1.00  0.00
ATOM     62  N   GLY   116       1.919   5.682   5.404  1.00  0.00
ATOM     63  CA  GLY   116       2.415   7.025   5.144  1.00  0.00
ATOM     64  C   GLY   116       2.515   7.950   6.341  1.00  0.00
ATOM     65  O   GLY   116       2.810   9.135   6.164  1.00  0.00
ATOM     66  N   HIS   117       2.264   7.457   7.550  1.00  0.00
ATOM     67  CA  HIS   117       2.382   8.317   8.746  1.00  0.00
ATOM     68  C   HIS   117       3.820   8.825   8.850  1.00  0.00
ATOM     69  O   HIS   117       4.770   8.109   8.527  1.00  0.00
ATOM     70  CB  HIS   117       2.033   7.528  10.010  1.00  0.00
ATOM     71  CG  HIS   117       1.869   8.382  11.229  1.00  0.00
ATOM     72  ND1 HIS   117       2.941   8.879  11.939  1.00  0.00
ATOM     73  CD2 HIS   117       0.741   8.910  11.984  1.00  0.00
ATOM     74  CE1 HIS   117       2.481   9.604  12.974  1.00  0.00
ATOM     75  NE2 HIS   117       1.163   9.626  13.007  1.00  0.00
ATOM     76  N   ILE   118       3.968  10.064   9.305  1.00  0.00
ATOM     77  CA  ILE   118       5.275  10.699   9.420  1.00  0.00
ATOM     78  C   ILE   118       5.727  10.882  10.864  1.00  0.00
ATOM     79  O   ILE   118       4.953  11.277  11.730  1.00  0.00
ATOM     80  CB  ILE   118       5.280  12.100   8.781  1.00  0.00
ATOM     81  CG1 ILE   118       4.971  12.005   7.285  1.00  0.00
ATOM     82  CG2 ILE   118       6.640  12.758   8.951  1.00  0.00
ATOM     83  CD1 ILE   118       4.720  13.344   6.627  1.00  0.00
ATOM     84  N   TYR   119       6.992  10.566  11.103  1.00  0.00
ATOM     85  CA  TYR   119       7.596  10.704  12.419  1.00  0.00
ATOM     86  C   TYR   119       8.911  11.438  12.265  1.00  0.00
ATOM     87  O   TYR   119       9.357  11.771  11.152  1.00  0.00
ATOM     88  CB  TYR   119       7.847   9.328  13.040  1.00  0.00
ATOM     89  CG  TYR   119       6.593   8.508  13.240  1.00  0.00
ATOM     90  CD1 TYR   119       6.166   7.612  12.268  1.00  0.00
ATOM     91  CD2 TYR   119       5.841   8.631  14.401  1.00  0.00
ATOM     92  CE1 TYR   119       5.021   6.859  12.442  1.00  0.00
ATOM     93  CE2 TYR   119       4.693   7.885  14.593  1.00  0.00
ATOM     94  CZ  TYR   119       4.287   6.994  13.600  1.00  0.00
ATOM     95  OH  TYR   119       3.146   6.245  13.776  1.00  0.00
ATOM     96  N   TYR   120       9.535  11.694  13.397  1.00  0.00
ATOM     97  CA  TYR   120      10.822  12.342  13.399  1.00  0.00
ATOM     98  C   TYR   120      11.615  11.765  14.562  1.00  0.00
ATOM     99  O   TYR   120      11.161  11.790  15.712  1.00  0.00
ATOM    100  CB  TYR   120      10.660  13.854  13.572  1.00  0.00
ATOM    101  CG  TYR   120      11.965  14.617  13.546  1.00  0.00
ATOM    102  CD1 TYR   120      12.635  14.839  12.351  1.00  0.00
ATOM    103  CD2 TYR   120      12.521  15.113  14.718  1.00  0.00
ATOM    104  CE1 TYR   120      13.829  15.536  12.318  1.00  0.00
ATOM    105  CE2 TYR   120      13.714  15.811  14.704  1.00  0.00
ATOM    106  CZ  TYR   120      14.366  16.020  13.491  1.00  0.00
ATOM    107  OH  TYR   120      15.555  16.713  13.461  1.00  0.00
ATOM    108  N   ILE   121      12.790  11.228  14.251  1.00  0.00
ATOM    109  CA  ILE   121      13.634  10.587  15.251  1.00  0.00
ATOM    110  C   ILE   121      14.030  11.462  16.432  1.00  0.00
ATOM    111  O   ILE   121      14.228  10.962  17.536  1.00  0.00
ATOM    112  CB  ILE   121      14.964  10.105  14.642  1.00  0.00
ATOM    113  CG1 ILE   121      14.704   9.066  13.549  1.00  0.00
ATOM    114  CG2 ILE   121      15.839   9.470  15.711  1.00  0.00
ATOM    115  CD1 ILE   121      15.937   8.692  12.756  1.00  0.00
TER
END
