
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0386TS383_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   21 , name T0386_D2.pdb
# PARAMETERS: T0386TS383_1-D2.T0386_D2.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:    21       219 - 239         4.52     4.52
  LCS_AVERAGE:     25.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       224 - 237         1.47     6.57
  LCS_AVERAGE:     13.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       224 - 234         0.70     6.50
  LCS_AVERAGE:      9.29

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:   81
LCS_GDT     N     219     N     219      4    4   21     3    4    4    4    4    6    8   10   10   12   13   19   20   21   21   21   21   21   21   21 
LCS_GDT     P     220     P     220      4    4   21     3    4    4    4    6    8   11   12   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     E     221     E     221      4    5   21     4    4    5    5    5    8   11   12   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     K     222     K     222      4    5   21     4    4    5    5    5    5    7    7    7   12   14   19   20   21   21   21   21   21   21   21 
LCS_GDT     I     223     I     223      4    5   21     4    4    5    5    5    5    7   11   14   15   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     R     224     R     224     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     L     225     L     225     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     L     226     L     226     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     K     227     K     227     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     E     228     E     228     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     F     229     F     229     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     M     230     M     230     11   14   21     6   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     H     231     H     231     11   14   21     5   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     T     232     T     232     11   14   21     4   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     M     233     M     233     11   14   21     4   10   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     K     234     K     234     11   14   21     4   10   11   12   13   14   14   14   15   16   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     N     235     N     235      4   14   21     3    3    4    7   13   14   14   14   15   16   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     T     236     T     236      4   14   21     3    6   11   12   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     G     237     G     237      3   14   21     3    3    3    8   13   14   14   14   15   16   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     R     238     R     238      3    4   21     3    3    3    4    4    4    9   11   15   15   17   19   20   21   21   21   21   21   21   21 
LCS_GDT     N     239     N     239      3    4   21     0    3    3    4    4    4    5    6   12   15   16   19   19   21   21   21   21   21   21   21 
LCS_AVERAGE  LCS_A:  16.19  (   9.29   13.35   25.93 )

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      6     10     11     12     13     14     14     14     15     16     17     19     20     21     21     21     21     21     21     21 
GDT PERCENT_CA   7.41  12.35  13.58  14.81  16.05  17.28  17.28  17.28  18.52  19.75  20.99  23.46  24.69  25.93  25.93  25.93  25.93  25.93  25.93  25.93
GDT RMS_LOCAL    0.27   0.63   0.70   0.96   1.24   1.47   1.47   1.47   2.27   3.07   3.37   4.26   4.29   4.52   4.52   4.52   4.52   4.52   4.52   4.52
GDT RMS_ALL_CA   6.27   6.50   6.50   6.53   6.56   6.57   6.57   6.57   6.56   5.37   5.31   4.60   4.63   4.52   4.52   4.52   4.52   4.52   4.52   4.52

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         15.641
LGA    P     220      P     220         11.461
LGA    E     221      E     221          9.528
LGA    K     222      K     222         11.887
LGA    I     223      I     223          8.434
LGA    R     224      R     224          1.169
LGA    L     225      L     225          1.196
LGA    L     226      L     226          0.914
LGA    K     227      K     227          1.017
LGA    E     228      E     228          1.002
LGA    F     229      F     229          0.781
LGA    M     230      M     230          0.918
LGA    H     231      H     231          1.207
LGA    T     232      T     232          0.373
LGA    M     233      M     233          0.974
LGA    K     234      K     234          1.842
LGA    N     235      N     235          3.001
LGA    T     236      T     236          1.411
LGA    G     237      G     237          2.503
LGA    R     238      R     238          7.817
LGA    N     239      N     239         11.621

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   81    4.0     14    1.47    17.593    16.933     0.891

LGA_LOCAL      RMSD =  1.472  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.567  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  4.518  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.060049 * X  +   0.939539 * Y  +  -0.337135 * Z  + -46.478493
  Y_new =  -0.977898 * X  +   0.123135 * Y  +   0.168979 * Z  +  56.419655
  Z_new =   0.200276 * X  +   0.319537 * Y  +   0.926167 * Z  +  63.104130 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.332222   -2.809370  [ DEG:    19.0349   -160.9651 ]
  Theta =  -0.201639   -2.939953  [ DEG:   -11.5531   -168.4469 ]
  Phi   =  -1.509468    1.632125  [ DEG:   -86.4861     93.5139 ]
 
# 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: T0386TS383_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS383_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   81   4.0   14   1.47  16.933     4.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS383_1-D2
PFRMAT TS
TARGET T0386
MODEL 1
PARENT 2g03A
ATOM    617  N   ASN   219       1.098  72.646  72.895  1.00  0.00
ATOM    618  CA  ASN   219       0.713  71.251  73.076  1.00  0.00
ATOM    619  C   ASN   219      -0.015  71.164  74.400  1.00  0.00
ATOM    620  O   ASN   219       0.324  71.878  75.329  1.00  0.00
ATOM    621  N   PRO   220      -1.019  70.303  74.517  1.00  0.00
ATOM    622  CA  PRO   220      -1.594  70.108  75.840  1.00  0.00
ATOM    623  C   PRO   220      -1.011  68.917  76.578  1.00  0.00
ATOM    624  O   PRO   220      -1.485  68.560  77.647  1.00  0.00
ATOM    625  N   GLU   221       0.050  68.342  76.028  1.00  0.00
ATOM    626  CA  GLU   221       0.732  67.227  76.678  1.00  0.00
ATOM    627  C   GLU   221       1.807  67.821  77.610  1.00  0.00
ATOM    628  O   GLU   221       2.998  67.676  77.361  1.00  0.00
ATOM    629  N   LYS   222       1.367  68.481  78.681  1.00  0.00
ATOM    630  CA  LYS   222       2.189  69.461  79.402  1.00  0.00
ATOM    631  C   LYS   222       3.276  68.820  80.280  1.00  0.00
ATOM    632  O   LYS   222       4.206  69.518  80.727  1.00  0.00
ATOM    633  N   ILE   223       3.156  67.514  80.514  1.00  0.00
ATOM    634  CA  ILE   223       4.049  66.802  81.423  1.00  0.00
ATOM    635  C   ILE   223       4.826  65.696  80.722  1.00  0.00
ATOM    636  O   ILE   223       5.436  64.857  81.365  1.00  0.00
ATOM    637  N   ARG   224       4.793  65.704  79.403  1.00  0.00
ATOM    638  CA  ARG   224       5.490  64.712  78.615  1.00  0.00
ATOM    639  C   ARG   224       7.016  64.897  78.708  1.00  0.00
ATOM    640  O   ARG   224       7.534  65.990  78.479  1.00  0.00
ATOM    641  N   LEU   225       7.727  63.837  79.086  1.00  0.00
ATOM    642  CA  LEU   225       9.179  63.904  79.257  1.00  0.00
ATOM    643  C   LEU   225       9.923  64.420  78.006  1.00  0.00
ATOM    644  O   LEU   225      10.847  65.218  78.127  1.00  0.00
ATOM    645  N   LEU   226       9.506  63.992  76.820  1.00  0.00
ATOM    646  CA  LEU   226      10.186  64.382  75.595  1.00  0.00
ATOM    647  C   LEU   226       9.986  65.869  75.270  1.00  0.00
ATOM    648  O   LEU   226      10.935  66.572  74.885  1.00  0.00
ATOM    649  N   LYS   227       8.755  66.352  75.435  1.00  0.00
ATOM    650  CA  LYS   227       8.443  67.764  75.251  1.00  0.00
ATOM    651  C   LYS   227       9.198  68.605  76.270  1.00  0.00
ATOM    652  O   LYS   227       9.781  69.630  75.911  1.00  0.00
ATOM    653  N   GLU   228       9.203  68.187  77.534  1.00  0.00
ATOM    654  CA  GLU   228       9.936  68.941  78.556  1.00  0.00
ATOM    655  C   GLU   228      11.455  68.981  78.228  1.00  0.00
ATOM    656  O   GLU   228      12.038  70.048  78.067  1.00  0.00
ATOM    657  N   PHE   229      12.079  67.827  78.074  1.00  0.00
ATOM    658  CA  PHE   229      13.528  67.791  77.922  1.00  0.00
ATOM    659  C   PHE   229      14.094  68.271  76.573  1.00  0.00
ATOM    660  O   PHE   229      15.109  68.950  76.568  1.00  0.00
ATOM    661  N   MET   230      13.447  67.934  75.457  1.00  0.00
ATOM    662  CA  MET   230      13.839  68.482  74.158  1.00  0.00
ATOM    663  C   MET   230      13.576  69.981  74.113  1.00  0.00
ATOM    664  O   MET   230      14.287  70.716  73.422  1.00  0.00
ATOM    665  N   HIS   231      12.561  70.430  74.857  1.00  0.00
ATOM    666  CA  HIS   231      12.240  71.837  74.993  1.00  0.00
ATOM    667  C   HIS   231      13.291  72.625  75.749  1.00  0.00
ATOM    668  O   HIS   231      13.669  73.713  75.330  1.00  0.00
ATOM    669  N   THR   232      13.734  72.103  76.890  1.00  0.00
ATOM    670  CA  THR   232      14.846  72.671  77.652  1.00  0.00
ATOM    671  C   THR   232      16.107  72.756  76.783  1.00  0.00
ATOM    672  O   THR   232      16.785  73.774  76.781  1.00  0.00
ATOM    673  N   MET   233      16.429  71.691  76.062  1.00  0.00
ATOM    674  CA  MET   233      17.552  71.748  75.132  1.00  0.00
ATOM    675  C   MET   233      17.420  72.845  74.071  1.00  0.00
ATOM    676  O   MET   233      18.404  73.494  73.745  1.00  0.00
ATOM    677  N   LYS   234      16.221  73.037  73.529  1.00  0.00
ATOM    678  CA  LYS   234      16.016  74.048  72.499  1.00  0.00
ATOM    679  C   LYS   234      16.116  75.442  73.115  1.00  0.00
ATOM    680  O   LYS   234      16.773  76.309  72.570  1.00  0.00
ATOM    681  N   ASN   235      15.474  75.642  74.264  1.00  0.00
ATOM    682  CA  ASN   235      15.547  76.883  75.015  1.00  0.00
ATOM    683  C   ASN   235      16.984  77.348  75.274  1.00  0.00
ATOM    684  O   ASN   235      17.303  78.538  75.117  1.00  0.00
ATOM    685  N   THR   236      17.838  76.417  75.691  1.00  0.00
ATOM    686  CA  THR   236      19.252  76.698  75.979  1.00  0.00
ATOM    687  C   THR   236      20.064  76.972  74.711  1.00  0.00
ATOM    688  O   THR   236      21.101  77.659  74.753  1.00  0.00
ATOM    689  N   GLY   237      19.590  76.432  73.592  1.00  0.00
ATOM    690  CA  GLY   237      20.187  76.690  72.277  1.00  0.00
ATOM    691  C   GLY   237      19.916  78.136  71.767  1.00  0.00
ATOM    692  O   GLY   237      20.759  78.732  71.096  1.00  0.00
ATOM    693  N   ARG   238      18.766  78.705  72.123  1.00  0.00
ATOM    694  CA  ARG   238      18.364  80.022  71.645  1.00  0.00
ATOM    695  C   ARG   238      19.392  81.064  72.015  1.00  0.00
ATOM    696  O   ARG   238      19.602  82.027  71.274  1.00  0.00
ATOM    697  N   ASN   239      20.061  80.889  73.148  1.00  0.00
ATOM    698  CA  ASN   239      21.022  81.927  73.527  1.00  0.00
ATOM    699  C   ASN   239      22.441  81.416  73.643  1.00  0.00
ATOM    700  O   ASN   239      23.239  82.017  74.339  1.00  0.00
TER
END
