
#######################################################
#                                                     #
#                        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 (  119),  selected   14 , name T0378TS389_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   14 , name T0378_D1.pdb
# PARAMETERS: T0378TS389_5-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:    14         5 - 77          4.07     4.07
  LCS_AVERAGE:     15.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11         5 - 15          0.89     5.53
  LCS_AVERAGE:     10.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11         5 - 15          0.89     5.53
  LCS_AVERAGE:     10.43

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     N       5     N       5     11   11   14     6    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     Q       6     Q       6     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     I       7     I       7     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     K       8     K       8     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     F       9     F       9     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     L      10     L      10     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     R      11     R      11     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     S      12     S      12     11   11   14     7    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     L      13     L      13     11   11   14     4    9   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     R      14     R      14     11   11   14     4    6   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     E      15     E      15     11   11   14     4    4   11   11   11   11   11   11   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     I      75     I      75      3    3   14     0    3    3    3    3    4    5    6    6    6    7    9   10   10   13   14   14   14   14   14 
LCS_GDT     S      76     S      76      3    3   14     0    3    3    3    3    4    6    8   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_GDT     T      77     T      77      3    3   14     0    3    3    3    9    9   10   10   11   12   13   13   13   13   13   14   14   14   14   14 
LCS_AVERAGE  LCS_A:  12.20  (  10.43   10.43   15.73 )

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      7      9     11     11     11     11     11     11     11     12     13     13     13     13     13     14     14     14     14     14 
GDT PERCENT_CA   7.87  10.11  12.36  12.36  12.36  12.36  12.36  12.36  12.36  13.48  14.61  14.61  14.61  14.61  14.61  15.73  15.73  15.73  15.73  15.73
GDT RMS_LOCAL    0.20   0.46   0.89   0.89   0.89   0.89   0.89   0.89   0.89   2.42   3.21   3.21   3.21   3.21   3.21   4.07   4.07   4.07   4.07   4.07
GDT RMS_ALL_CA   5.17   5.09   5.53   5.53   5.53   5.53   5.53   5.53   5.53   4.65   4.19   4.19   4.19   4.19   4.19   4.07   4.07   4.07   4.07   4.07

#      Molecule1      Molecule2       DISTANCE
LGA    N       5      N       5          0.905
LGA    Q       6      Q       6          0.387
LGA    I       7      I       7          0.549
LGA    K       8      K       8          0.463
LGA    F       9      F       9          0.545
LGA    L      10      L      10          0.820
LGA    R      11      R      11          1.007
LGA    S      12      S      12          0.771
LGA    L      13      L      13          0.741
LGA    R      14      R      14          1.315
LGA    E      15      E      15          1.558
LGA    I      75      I      75         13.801
LGA    S      76      S      76         11.821
LGA    T      77      T      77          9.439

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14   89    4.0     11    0.89    12.640    12.243     1.108

LGA_LOCAL      RMSD =  0.893  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.529  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  4.070  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.552779 * X  +  -0.434949 * Y  +  -0.710813 * Z  +  21.114082
  Y_new =  -0.021801 * X  +  -0.860237 * Y  +   0.509428 * Z  +  17.993269
  Z_new =  -0.833042 * X  +  -0.266105 * Y  +  -0.485003 * Z  +  56.146957 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.639773    0.501819  [ DEG:  -151.2479     28.7521 ]
  Theta =   0.984585    2.157008  [ DEG:    56.4126    123.5874 ]
  Phi   =  -0.039418    3.102175  [ DEG:    -2.2585    177.7415 ]
 
# 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: T0378TS389_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS389_5-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14   89   4.0   11   0.89  12.243     4.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS389_5-D1
PFRMAT TS
TARGET T0378
MODEL  5
PARENT N/A
ATOM      2  N   ASN     5       6.754  36.395  54.375  1.00  0.00
ATOM      3  CA  ASN     5       7.698  35.639  55.189  1.00  0.00
ATOM      4  CB  ASN     5       7.221  35.574  56.643  1.00  0.00
ATOM      5  CG  ASN     5       7.373  36.898  57.365  1.00  0.00
ATOM      6  ND2 ASN     5       6.644  37.059  58.462  1.00  0.00
ATOM      7  OD1 ASN     5       8.139  37.763  56.940  1.00  0.00
ATOM      8  O   ASN     5       8.952  33.694  54.548  1.00  0.00
ATOM      9  C   ASN     5       7.843  34.212  54.672  1.00  0.00
ATOM     10  N   GLN     6       6.712  33.583  54.368  1.00  0.00
ATOM     11  CA  GLN     6       6.713  32.215  53.870  1.00  0.00
ATOM     12  CB  GLN     6       5.281  31.737  53.618  1.00  0.00
ATOM     13  CG  GLN     6       4.472  31.505  54.884  1.00  0.00
ATOM     14  CD  GLN     6       3.038  31.107  54.596  1.00  0.00
ATOM     15  OE1 GLN     6       2.624  31.039  53.440  1.00  0.00
ATOM     16  NE2 GLN     6       2.276  30.843  55.651  1.00  0.00
ATOM     17  O   GLN     6       8.037  31.068  52.227  1.00  0.00
ATOM     18  C   GLN     6       7.488  32.120  52.558  1.00  0.00
ATOM     19  N   ILE     7       7.531  33.224  51.817  1.00  0.00
ATOM     20  CA  ILE     7       8.250  33.270  50.548  1.00  0.00
ATOM     21  CB  ILE     7       7.988  34.589  49.797  1.00  0.00
ATOM     22  CG1 ILE     7       6.530  34.662  49.341  1.00  0.00
ATOM     23  CG2 ILE     7       8.884  34.692  48.574  1.00  0.00
ATOM     24  CD1 ILE     7       6.119  36.026  48.830  1.00  0.00
ATOM     25  O   ILE     7      10.481  32.526  50.056  1.00  0.00
ATOM     26  C   ILE     7       9.743  33.148  50.821  1.00  0.00
ATOM     27  N   LYS     8      10.179  33.756  51.922  1.00  0.00
ATOM     28  CA  LYS     8      11.580  33.737  52.315  1.00  0.00
ATOM     29  CB  LYS     8      11.798  34.590  53.565  1.00  0.00
ATOM     30  CG  LYS     8      11.654  36.084  53.331  1.00  0.00
ATOM     31  CD  LYS     8      11.883  36.871  54.611  1.00  0.00
ATOM     32  CE  LYS     8      11.717  38.365  54.380  1.00  0.00
ATOM     33  NZ  LYS     8      11.908  39.143  55.634  1.00  0.00
ATOM     34  O   LYS     8      13.144  31.922  52.197  1.00  0.00
ATOM     35  C   LYS     8      12.062  32.325  52.626  1.00  0.00
ATOM     36  N   PHE     9      11.259  31.575  53.374  1.00  0.00
ATOM     37  CA  PHE     9      11.624  30.211  53.738  1.00  0.00
ATOM     38  CB  PHE     9      10.577  29.610  54.678  1.00  0.00
ATOM     39  CG  PHE     9      10.697  30.079  56.100  1.00  0.00
ATOM     40  CD1 PHE     9       9.853  31.055  56.595  1.00  0.00
ATOM     41  CD2 PHE     9      11.655  29.540  56.942  1.00  0.00
ATOM     42  CE1 PHE     9       9.965  31.488  57.904  1.00  0.00
ATOM     43  CE2 PHE     9      11.766  29.970  58.250  1.00  0.00
ATOM     44  CZ  PHE     9      10.927  30.941  58.733  1.00  0.00
ATOM     45  O   PHE     9      12.627  28.530  52.348  1.00  0.00
ATOM     46  C   PHE     9      11.713  29.343  52.486  1.00  0.00
ATOM     47  N   LEU    10      10.765  29.523  51.569  1.00  0.00
ATOM     48  CA  LEU    10      10.756  28.765  50.323  1.00  0.00
ATOM     49  CB  LEU    10       9.481  29.056  49.528  1.00  0.00
ATOM     50  CG  LEU    10       8.175  28.527  50.124  1.00  0.00
ATOM     51  CD1 LEU    10       6.978  29.036  49.336  1.00  0.00
ATOM     52  CD2 LEU    10       8.148  27.006  50.097  1.00  0.00
ATOM     53  O   LEU    10      12.549  28.313  48.791  1.00  0.00
ATOM     54  C   LEU    10      11.960  29.151  49.477  1.00  0.00
ATOM     55  N   ARG    11      12.319  30.429  49.532  1.00  0.00
ATOM     56  CA  ARG    11      13.462  30.942  48.790  1.00  0.00
ATOM     57  CB  ARG    11      13.584  32.456  48.975  1.00  0.00
ATOM     58  CG  ARG    11      14.714  33.089  48.179  1.00  0.00
ATOM     59  CD  ARG    11      14.837  34.575  48.479  1.00  0.00
ATOM     60  NE  ARG    11      15.245  34.821  49.860  1.00  0.00
ATOM     61  CZ  ARG    11      16.492  34.697  50.304  1.00  0.00
ATOM     62  NH1 ARG    11      16.770  34.943  51.576  1.00  0.00
ATOM     63  NH2 ARG    11      17.458  34.330  49.473  1.00  0.00
ATOM     64  O   ARG    11      15.559  29.776  48.586  1.00  0.00
ATOM     65  C   ARG    11      14.702  30.245  49.335  1.00  0.00
ATOM     66  N   SER    12      14.778  30.177  50.659  1.00  0.00
ATOM     67  CA  SER    12      15.903  29.550  51.330  1.00  0.00
ATOM     68  CB  SER    12      15.819  29.775  52.841  1.00  0.00
ATOM     69  OG  SER    12      15.971  31.146  53.163  1.00  0.00
ATOM     70  O   SER    12      16.965  27.441  50.899  1.00  0.00
ATOM     71  C   SER    12      15.909  28.048  51.064  1.00  0.00
ATOM     72  N   LEU    13      14.718  27.461  51.009  1.00  0.00
ATOM     73  CA  LEU    13      14.577  26.032  50.759  1.00  0.00
ATOM     74  CB  LEU    13      13.105  25.621  50.815  1.00  0.00
ATOM     75  CG  LEU    13      12.806  24.137  50.586  1.00  0.00
ATOM     76  CD1 LEU    13      13.475  23.284  51.653  1.00  0.00
ATOM     77  CD2 LEU    13      11.309  23.876  50.636  1.00  0.00
ATOM     78  O   LEU    13      15.816  24.729  49.161  1.00  0.00
ATOM     79  C   LEU    13      15.141  25.732  49.371  1.00  0.00
ATOM     80  N   ARG    14      14.858  26.619  48.425  1.00  0.00
ATOM     81  CA  ARG    14      15.334  26.449  47.062  1.00  0.00
ATOM     82  CB  ARG    14      14.834  27.587  46.173  1.00  0.00
ATOM     83  CG  ARG    14      13.342  27.540  45.884  1.00  0.00
ATOM     84  CD  ARG    14      12.904  28.724  45.037  1.00  0.00
ATOM     85  NE  ARG    14      11.464  28.718  44.792  1.00  0.00
ATOM     86  CZ  ARG    14      10.816  29.669  44.126  1.00  0.00
ATOM     87  NH1 ARG    14       9.504  29.581  43.952  1.00  0.00
ATOM     88  NH2 ARG    14      11.481  30.706  43.636  1.00  0.00
ATOM     89  O   ARG    14      17.471  25.597  46.368  1.00  0.00
ATOM     90  C   ARG    14      16.863  26.443  47.016  1.00  0.00
ATOM     91  N   GLU    15      17.478  27.396  47.707  1.00  0.00
ATOM     92  CA  GLU    15      18.936  27.481  47.754  1.00  0.00
ATOM     93  CB  GLU    15      19.375  28.666  48.616  1.00  0.00
ATOM     94  CG  GLU    15      19.101  30.024  47.992  1.00  0.00
ATOM     95  CD  GLU    15      19.436  31.172  48.922  1.00  0.00
ATOM     96  OE1 GLU    15      19.812  30.906  50.084  1.00  0.00
ATOM     97  OE2 GLU    15      19.323  32.339  48.492  1.00  0.00
ATOM     98  O   GLU    15      20.517  25.670  47.892  1.00  0.00
ATOM     99  C   GLU    15      19.501  26.196  48.351  1.00  0.00
ATOM    100  N   ILE    75      18.836  25.694  49.382  1.00  0.00
ATOM    101  CA  ILE    75      19.265  24.463  50.030  1.00  0.00
ATOM    102  CB  ILE    75      18.419  24.157  51.278  1.00  0.00
ATOM    103  CG1 ILE    75      18.676  25.202  52.367  1.00  0.00
ATOM    104  CG2 ILE    75      18.768  22.784  51.836  1.00  0.00
ATOM    105  CD1 ILE    75      17.698  25.135  53.519  1.00  0.00
ATOM    106  O   ILE    75      20.039  22.481  48.933  1.00  0.00
ATOM    107  C   ILE    75      19.128  23.295  49.061  1.00  0.00
ATOM    108  N   SER    76      17.993  23.211  48.372  1.00  0.00
ATOM    109  CA  SER    76      17.790  22.119  47.427  1.00  0.00
ATOM    110  CB  SER    76      16.393  22.201  46.808  1.00  0.00
ATOM    111  OG  SER    76      16.256  23.364  46.010  1.00  0.00
ATOM    112  O   SER    76      19.194  21.118  45.753  1.00  0.00
ATOM    113  C   SER    76      18.809  22.159  46.287  1.00  0.00
ATOM    114  N   THR    77      19.268  23.353  45.926  1.00  0.00
ATOM    115  CA  THR    77      20.246  23.478  44.850  1.00  0.00
ATOM    116  CB  THR    77      20.434  24.945  44.423  1.00  0.00
ATOM    117  CG2 THR    77      19.119  25.526  43.923  1.00  0.00
ATOM    118  OG1 THR    77      20.885  25.717  45.542  1.00  0.00
ATOM    119  O   THR    77      22.494  22.776  44.380  1.00  0.00
ATOM    120  C   THR    77      21.632  22.958  45.236  1.00  0.00
TER
END
