
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0353AL381_5
# Molecule2: number of CA atoms   85 ( 1334),  selected   19 , name T0353.pdb
# PARAMETERS: T0353AL381_5.T0353.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:    19        64 - 82          4.14     4.14
  LCS_AVERAGE:     22.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        64 - 76          1.52     9.19
  LCS_AVERAGE:     13.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        64 - 75          0.92    10.40
  LCS_AVERAGE:     11.46

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:   85
LCS_GDT     P      64     P      64     12   13   19     8   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     D      65     D      65     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     E      66     E      66     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     V      67     V      67     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     I      68     I      68     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     E      69     E      69     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     A      70     A      70     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     I      71     I      71     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     K      72     K      72     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     Q      73     Q      73     12   13   19     9   10   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     N      74     N      74     12   13   19     3    8   11   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     G      75     G      75     12   13   19     3    5   10   12   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     Y      76     Y      76      5   13   19     3    5    6    8   12   13   13   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     F      77     F      77      6    8   19     3    5    6    7    8   10   11   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     I      78     I      78      6    8   19     4    5    6    7    8   10   11   14   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     Y      79     Y      79      6    8   19     4    5    6    7    8   10   11   13   16   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     K      80     K      80      6    8   19     4    5    6    7    8    8   10   10   13   15   16   17   18   19   19   19   19   19   19   19 
LCS_GDT     M      81     M      81      6    8   19     4    5    6    7    8    8   10   12   15   16   17   17   18   19   19   19   19   19   19   19 
LCS_GDT     E      82     E      82      6    8   19     0    3    6    7    8    8   10   10   13   15   16   16   18   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  15.75  (  11.46   13.44   22.35 )

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      9     10     11     12     12     13     13     14     16     16     17     17     18     19     19     19     19     19     19     19 
GDT PERCENT_CA  10.59  11.76  12.94  14.12  14.12  15.29  15.29  16.47  18.82  18.82  20.00  20.00  21.18  22.35  22.35  22.35  22.35  22.35  22.35  22.35
GDT RMS_LOCAL    0.34   0.38   0.54   0.92   0.92   1.52   1.52   2.64   3.26   3.26   3.49   3.49   3.83   4.14   4.14   4.14   4.14   4.14   4.14   4.14
GDT RMS_ALL_CA  10.93  11.01  10.78  10.40  10.40   9.19   9.19   7.04   4.82   4.82   4.44   4.44   4.26   4.14   4.14   4.14   4.14   4.14   4.14   4.14

#      Molecule1      Molecule2       DISTANCE
LGA    P      64      P      64          3.399
LGA    D      65      D      65          2.481
LGA    E      66      E      66          3.270
LGA    V      67      V      67          3.652
LGA    I      68      I      68          3.293
LGA    E      69      E      69          2.898
LGA    A      70      A      70          2.782
LGA    I      71      I      71          3.316
LGA    K      72      K      72          3.472
LGA    Q      73      Q      73          2.310
LGA    N      74      N      74          1.520
LGA    G      75      G      75          2.063
LGA    Y      76      Y      76          1.799
LGA    F      77      F      77          3.911
LGA    I      78      I      78          4.130
LGA    Y      79      Y      79          6.288
LGA    K      80      K      80         10.392
LGA    M      81      M      81          7.595
LGA    E      82      E      82         12.715

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   85    4.0     14    2.64    16.176    15.784     0.511

LGA_LOCAL      RMSD =  2.641  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.161  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  4.142  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.159435 * X  +   0.105962 * Y  +  -0.981505 * Z  +   6.830726
  Y_new =  -0.094506 * X  +  -0.988019 * Y  +  -0.122017 * Z  + -10.496629
  Z_new =  -0.982674 * X  +   0.112211 * Y  +  -0.147511 * Z  +   1.460192 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.491279   -0.650314  [ DEG:   142.7398    -37.2602 ]
  Theta =   1.384379    1.757214  [ DEG:    79.3191    100.6809 ]
  Phi   =  -0.535073    2.606520  [ DEG:   -30.6574    149.3426 ]
 
# 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: T0353AL381_5                                  
REMARK     2: T0353.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0353AL381_5.T0353.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   85   4.0   14   2.64  15.784     4.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL381_5
REMARK Aligment from pdb entry: 1mwyA
ATOM      1  N   PRO    64      15.570  -7.785  -0.218  1.00  0.00              
ATOM      2  CA  PRO    64      14.313  -7.070  -0.003  1.00  0.00              
ATOM      3  C   PRO    64      13.767  -6.519  -1.305  1.00  0.00              
ATOM      4  O   PRO    64      12.580  -6.661  -1.588  1.00  0.00              
ATOM      5  N   ASP    65      14.655  -5.936  -2.110  1.00  0.00              
ATOM      6  CA  ASP    65      14.320  -5.463  -3.440  1.00  0.00              
ATOM      7  C   ASP    65      13.791  -6.622  -4.280  1.00  0.00              
ATOM      8  O   ASP    65      12.938  -6.433  -5.147  1.00  0.00              
ATOM      9  N   GLU    66      14.299  -7.834  -4.026  1.00  0.00              
ATOM     10  CA  GLU    66      13.910  -8.985  -4.803  1.00  0.00              
ATOM     11  C   GLU    66      12.494  -9.384  -4.415  1.00  0.00              
ATOM     12  O   GLU    66      11.650  -9.626  -5.281  1.00  0.00              
ATOM     13  N   VAL    67      12.223  -9.416  -3.109  1.00  0.00              
ATOM     14  CA  VAL    67      10.906  -9.782  -2.645  1.00  0.00              
ATOM     15  C   VAL    67       9.910  -8.714  -3.100  1.00  0.00              
ATOM     16  O   VAL    67       8.859  -9.043  -3.642  1.00  0.00              
ATOM     17  N   ILE    68      10.240  -7.433  -2.899  1.00  0.00              
ATOM     18  CA  ILE    68       9.468  -6.344  -3.479  1.00  0.00              
ATOM     19  C   ILE    68       9.176  -6.591  -4.947  1.00  0.00              
ATOM     20  O   ILE    68       8.008  -6.666  -5.289  1.00  0.00              
ATOM     21  N   GLU    69      10.187  -6.742  -5.808  1.00  0.00              
ATOM     22  CA  GLU    69       9.956  -6.987  -7.230  1.00  0.00              
ATOM     23  C   GLU    69       8.930  -8.113  -7.417  1.00  0.00              
ATOM     24  O   GLU    69       8.016  -8.016  -8.238  1.00  0.00              
ATOM     25  N   ALA    70       9.078  -9.184  -6.637  1.00  0.00              
ATOM     26  CA  ALA    70       8.166 -10.311  -6.649  1.00  0.00              
ATOM     27  C   ALA    70       6.727  -9.905  -6.302  1.00  0.00              
ATOM     28  O   ALA    70       5.781 -10.289  -6.985  1.00  0.00              
ATOM     29  N   ILE    71       6.548  -9.147  -5.222  1.00  0.00              
ATOM     30  CA  ILE    71       5.246  -8.759  -4.703  1.00  0.00              
ATOM     31  C   ILE    71       4.591  -7.740  -5.628  1.00  0.00              
ATOM     32  O   ILE    71       3.395  -7.814  -5.918  1.00  0.00              
ATOM     33  N   LYS    72       5.411  -6.838  -6.154  1.00  0.00              
ATOM     34  CA  LYS    72       5.029  -5.980  -7.260  1.00  0.00              
ATOM     35  C   LYS    72       4.469  -6.815  -8.420  1.00  0.00              
ATOM     36  O   LYS    72       3.310  -6.618  -8.780  1.00  0.00              
ATOM     37  N   GLN    73       5.222  -7.777  -8.979  1.00  0.00              
ATOM     38  CA  GLN    73       4.673  -8.577 -10.082  1.00  0.00              
ATOM     39  C   GLN    73       3.422  -9.355  -9.649  1.00  0.00              
ATOM     40  O   GLN    73       2.500  -9.535 -10.439  1.00  0.00              
ATOM     41  N   ASN    74       3.388  -9.823  -8.396  1.00  0.00              
ATOM     42  CA  ASN    74       2.237 -10.529  -7.845  1.00  0.00              
ATOM     43  C   ASN    74       1.004  -9.623  -7.754  1.00  0.00              
ATOM     44  O   ASN    74      -0.118 -10.126  -7.686  1.00  0.00              
ATOM     45  N   GLY    75       1.209  -8.302  -7.760  1.00  0.00              
ATOM     46  CA  GLY    75       0.155  -7.308  -7.847  1.00  0.00              
ATOM     47  C   GLY    75      -0.182  -6.730  -6.478  1.00  0.00              
ATOM     48  O   GLY    75      -1.350  -6.457  -6.208  1.00  0.00              
ATOM     49  N   TYR    76       0.827  -6.526  -5.625  1.00  0.00              
ATOM     50  CA  TYR    76       0.658  -5.875  -4.335  1.00  0.00              
ATOM     51  C   TYR    76       1.664  -4.734  -4.214  1.00  0.00              
ATOM     52  O   TYR    76       2.872  -4.953  -4.302  1.00  0.00              
ATOM     53  N   PHE    77       1.168  -3.520  -3.981  1.00  0.00              
ATOM     54  CA  PHE    77       2.009  -2.368  -3.726  1.00  0.00              
ATOM     55  C   PHE    77       2.407  -2.426  -2.256  1.00  0.00              
ATOM     56  O   PHE    77       1.547  -2.314  -1.381  1.00  0.00              
ATOM     57  N   ILE    78       3.702  -2.618  -1.998  1.00  0.00              
ATOM     58  CA  ILE    78       4.265  -2.560  -0.663  1.00  0.00              
ATOM     59  C   ILE    78       5.151  -1.335  -0.498  1.00  0.00              
ATOM     60  O   ILE    78       5.327  -0.548  -1.429  1.00  0.00              
ATOM     61  N   TYR    79       5.721  -1.198   0.696  1.00  0.00              
ATOM     62  CA  TYR    79       6.838  -0.332   0.981  1.00  0.00              
ATOM     63  C   TYR    79       7.810  -1.190   1.774  1.00  0.00              
ATOM     64  O   TYR    79       7.402  -1.863   2.726  1.00  0.00              
ATOM     65  N   LYS    80       9.062  -1.203   1.323  1.00  0.00              
ATOM     66  CA  LYS    80      10.157  -1.912   1.923  1.00  0.00              
ATOM     67  C   LYS    80      10.392  -1.308   3.288  1.00  0.00              
ATOM     68  O   LYS    80      10.725  -0.125   3.380  1.00  0.00              
ATOM     69  N   MET    81      10.181  -2.102   4.330  1.00  0.00              
ATOM     70  CA  MET    81      10.492  -1.661   5.672  1.00  0.00              
ATOM     71  C   MET    81      11.909  -2.021   6.085  1.00  0.00              
ATOM     72  O   MET    81      12.600  -2.836   5.476  1.00  0.00              
ATOM     73  N   GLU    82      12.322  -1.369   7.167  1.00  0.00              
ATOM     74  CA  GLU    82      13.607  -1.620   7.796  1.00  0.00              
ATOM     75  C   GLU    82      13.679  -3.055   8.342  1.00  0.00              
ATOM     76  O   GLU    82      12.677  -3.774   8.408  1.00  0.00              
END
