
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0378AL243_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   11 , name T0378_D1.pdb
# PARAMETERS: T0378AL243_4-D1.T0378_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        79 - 88          4.93     5.60
  LONGEST_CONTINUOUS_SEGMENT:    10        80 - 89          4.84     5.66
  LCS_AVERAGE:     11.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        81 - 84          1.57    10.20
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.99     8.87
  LCS_AVERAGE:      3.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.99     8.87
  LCS_AVERAGE:      3.78

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:   89
LCS_GDT     T      79     T      79      3    3   10     3    3    3    3    3    4    4    5    5    6    7    7   10   10   10   11   11   11   11   11 
LCS_GDT     T      80     T      80      3    3   10     3    3    3    3    3    4    4    5    6    6    7    9   10   10   10   11   11   11   11   11 
LCS_GDT     P      81     P      81      3    4   10     3    3    3    4    4    5    5    6    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     Q      82     Q      82      4    4   10     3    3    4    4    4    5    5    6    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     P      83     P      83      4    4   10     3    3    4    4    4    5    5    6    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     L      84     L      84      4    4   10     3    3    4    4    4    5    5    6    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     M      85     M      85      4    4   10     1    3    4    4    4    5    5    6    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     A      86     A      86      3    3   10     3    3    3    3    3    3    5    6    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     V      87     V      87      3    3   10     3    3    3    3    3    3    4    5    7    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     F      88     F      88      3    3   10     3    3    3    3    3    3    4    5    6    8    8    9   10   10   10   11   11   11   11   11 
LCS_GDT     D      89     D      89      3    3   10     0    3    3    3    3    3    4    4    5    6    7    8    9    9   10   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   6.30  (   3.78    3.88   11.24 )

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      3      3      4      4      4      5      5      6      7      8      8      9     10     10     10     11     11     11     11     11 
GDT PERCENT_CA   3.37   3.37   4.49   4.49   4.49   5.62   5.62   6.74   7.87   8.99   8.99  10.11  11.24  11.24  11.24  12.36  12.36  12.36  12.36  12.36
GDT RMS_LOCAL    0.08   0.08   0.99   0.99   0.99   2.04   2.04   2.95   3.59   3.84   3.84   4.38   4.93   4.93   4.84   5.38   5.38   5.38   5.38   5.38
GDT RMS_ALL_CA  16.44  16.44   8.87   8.87   8.87   7.73   7.73   6.39   6.40   6.38   6.38   5.74   5.60   5.60   5.66   5.38   5.38   5.38   5.38   5.38

#      Molecule1      Molecule2       DISTANCE
LGA    T      79      T      79         11.176
LGA    T      80      T      80          6.680
LGA    P      81      P      81          2.031
LGA    Q      82      Q      82          3.288
LGA    P      83      P      83          2.117
LGA    L      84      L      84          3.709
LGA    M      85      M      85          2.916
LGA    A      86      A      86          3.982
LGA    V      87      V      87          7.885
LGA    F      88      F      88          7.380
LGA    D      89      D      89          8.974

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   89    4.0      6    2.95     6.742     6.115     0.197

LGA_LOCAL      RMSD =  2.951  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.210  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  5.384  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.316127 * X  +   0.948598 * Y  +   0.014991 * Z  +  -6.419259
  Y_new =   0.156580 * X  +  -0.036583 * Y  +  -0.986988 * Z  +  26.958918
  Z_new =  -0.935706 * X  +   0.314361 * Y  +  -0.160096 * Z  +  70.213242 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.041837   -1.099756  [ DEG:   116.9886    -63.0114 ]
  Theta =   1.210256    1.931337  [ DEG:    69.3426    110.6574 ]
  Phi   =   0.459886   -2.681707  [ DEG:    26.3495   -153.6505 ]
 
# 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: T0378AL243_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL243_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   89   4.0    6   2.95   6.115     5.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL243_4-D1
REMARK Aligment from pdb entry: 1v2xA
ATOM      1  N   THR    79       1.115  24.976  36.048  1.00  0.00              
ATOM      2  CA  THR    79       0.597  23.651  36.347  1.00  0.00              
ATOM      3  C   THR    79       1.580  22.843  37.196  1.00  0.00              
ATOM      4  O   THR    79       1.187  22.072  38.073  1.00  0.00              
ATOM      5  N   THR    80       2.866  23.042  36.945  1.00  0.00              
ATOM      6  CA  THR    80       3.879  22.288  37.655  1.00  0.00              
ATOM      7  C   THR    80       4.656  23.148  38.666  1.00  0.00              
ATOM      8  O   THR    80       4.689  22.841  39.857  1.00  0.00              
ATOM      9  N   PRO    81       5.242  24.242  38.201  1.00  0.00              
ATOM     10  CA  PRO    81       6.021  25.116  39.072  1.00  0.00              
ATOM     11  C   PRO    81       5.216  25.609  40.262  1.00  0.00              
ATOM     12  O   PRO    81       5.779  25.906  41.308  1.00  0.00              
ATOM     13  N   GLN    82       3.900  25.680  40.120  1.00  0.00              
ATOM     14  CA  GLN    82       3.085  26.173  41.220  1.00  0.00              
ATOM     15  C   GLN    82       2.359  25.090  42.007  1.00  0.00              
ATOM     16  O   GLN    82       2.859  24.603  43.019  1.00  0.00              
ATOM     17  N   PRO    83       1.169  24.735  41.537  1.00  0.00              
ATOM     18  CA  PRO    83       0.342  23.736  42.183  1.00  0.00              
ATOM     19  C   PRO    83       1.178  22.530  42.597  1.00  0.00              
ATOM     20  O   PRO    83       1.241  22.182  43.773  1.00  0.00              
ATOM     21  N   LEU    84       1.828  21.917  41.613  1.00  0.00              
ATOM     22  CA  LEU    84       2.659  20.741  41.816  1.00  0.00              
ATOM     23  C   LEU    84       3.697  20.896  42.936  1.00  0.00              
ATOM     24  O   LEU    84       3.742  20.081  43.854  1.00  0.00              
ATOM     25  N   MET    85       4.512  21.942  42.853  1.00  0.00              
ATOM     26  CA  MET    85       5.571  22.220  43.831  1.00  0.00              
ATOM     27  C   MET    85       5.062  22.576  45.231  1.00  0.00              
ATOM     28  O   MET    85       5.595  22.067  46.221  1.00  0.00              
ATOM     29  N   ALA    86       4.048  23.435  45.336  1.00  0.00              
ATOM     30  CA  ALA    86       3.546  23.789  46.662  1.00  0.00              
ATOM     31  C   ALA    86       2.880  22.598  47.364  1.00  0.00              
ATOM     32  O   ALA    86       3.024  22.426  48.569  1.00  0.00              
ATOM     33  N   VAL    87       2.152  21.773  46.618  1.00  0.00              
ATOM     34  CA  VAL    87       1.496  20.619  47.212  1.00  0.00              
ATOM     35  C   VAL    87       2.511  19.599  47.761  1.00  0.00              
ATOM     36  O   VAL    87       2.302  18.981  48.816  1.00  0.00              
ATOM     37  N   PHE    88       3.605  19.401  47.039  1.00  0.00              
ATOM     38  CA  PHE    88       4.577  18.424  47.489  1.00  0.00              
ATOM     39  C   PHE    88       5.286  19.012  48.674  1.00  0.00              
ATOM     40  O   PHE    88       5.613  18.295  49.611  1.00  0.00              
ATOM     41  N   ASP    89       5.534  20.311  48.632  1.00  0.00              
ATOM     42  CA  ASP    89       6.214  20.961  49.748  1.00  0.00              
ATOM     43  C   ASP    89       5.465  20.667  51.038  1.00  0.00              
ATOM     44  O   ASP    89       6.067  20.331  52.059  1.00  0.00              
END
