
#######################################################
#                                                     #
#                        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    5 (   39),  selected    5 , name T0298TS671_5-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    5 , name T0298_D1.pdb
# PARAMETERS: T0298TS671_5-D1.T0298_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:     5       129 - 319         0.93     0.93
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       129 - 319         0.93     0.93
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       129 - 319         0.93     0.93
  LCS_AVERAGE:      3.38

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:  148
LCS_GDT     P     129     P     129      5    5    5     0    3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     316     V     316      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     R     317     R     317      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     318     K     318      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     319     G     319      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.38  (   3.38    3.38    3.38 )

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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   2.70   2.70   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38
GDT RMS_LOCAL    0.37   0.37   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93
GDT RMS_ALL_CA   1.69   1.69   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93

#      Molecule1      Molecule2       DISTANCE
LGA    P     129      P     129          1.230
LGA    V     316      V     316          0.404
LGA    R     317      R     317          0.439
LGA    K     318      K     318          1.209
LGA    G     319      G     319          0.980

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  148    4.0      5    0.93     3.209     3.325     0.487

LGA_LOCAL      RMSD =  0.927  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.927  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.927  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.343315 * X  +   0.924860 * Y  +   0.163613 * Z  + -45.739414
  Y_new =   0.027915 * X  +   0.184172 * Y  +  -0.982498 * Z  +  55.004784
  Z_new =  -0.938805 * X  +  -0.332739 * Y  +  -0.089047 * Z  + -28.088804 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.832286    1.309306  [ DEG:  -104.9823     75.0177 ]
  Theta =   1.219146    1.922447  [ DEG:    69.8519    110.1481 ]
  Phi   =   3.060460   -0.081133  [ DEG:   175.3514     -4.6486 ]
 
# 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: T0298TS671_5-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS671_5-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  148   4.0    5   0.93   3.325     0.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS671_5-D1
PFRMAT TS
TARGET T0298
MODEL  5  REFINED
PARENT 1PQP_A 1MB4_B 1T4B_B
ATOM      1  N   PRO   129     -13.966  77.161  -1.088  1.00  0.00
ATOM      2  CA  PRO   129     -14.058  75.755  -0.970  1.00  0.00
ATOM      3  C   PRO   129     -12.937  75.124  -0.051  1.00  0.00
ATOM      4  O   PRO   129     -13.097  73.938   0.246  1.00  0.00
ATOM      5  CB  PRO   129     -13.848  75.193  -2.392  1.00  0.00
ATOM      6  CG  PRO   129     -12.807  76.175  -2.923  1.00  0.00
ATOM      7  CD  PRO   129     -13.052  77.514  -2.209  1.00  0.00
ATOM   1402  N   VAL   316     -13.544  65.572   4.536  1.00  0.00
ATOM   1403  CA  VAL   316     -14.169  65.019   3.358  1.00  0.00
ATOM   1404  C   VAL   316     -15.636  65.514   3.199  1.00  0.00
ATOM   1405  O   VAL   316     -16.069  65.503   1.997  1.00  0.00
ATOM   1406  CB  VAL   316     -14.138  63.484   3.426  1.00  0.00
ATOM   1407  CG1 VAL   316     -13.030  62.930   4.338  1.00  0.00
ATOM   1408  CG2 VAL   316     -15.385  62.672   3.849  1.00  0.00
ATOM   1409  N   ARG   317     -16.527  65.336   4.201  1.00  0.00
ATOM   1410  CA  ARG   317     -17.920  65.729   4.096  1.00  0.00
ATOM   1411  C   ARG   317     -18.221  67.231   3.750  1.00  0.00
ATOM   1412  O   ARG   317     -18.409  67.501   2.554  1.00  0.00
ATOM   1413  CB  ARG   317     -18.600  65.453   5.421  1.00  0.00
ATOM   1414  CG  ARG   317     -18.727  64.038   5.841  1.00  0.00
ATOM   1415  CD  ARG   317     -19.757  63.284   5.046  1.00  0.00
ATOM   1416  NE  ARG   317     -19.917  61.888   5.405  1.00  0.00
ATOM   1417  CZ  ARG   317     -19.024  60.904   5.142  1.00  0.00
ATOM   1418  NH1 ARG   317     -17.836  61.137   4.515  1.00  0.00
ATOM   1419  NH2 ARG   317     -19.354  59.652   5.508  1.00  0.00
ATOM   1420  N   LYS   318     -17.880  68.210   4.616  1.00  0.00
ATOM   1421  CA  LYS   318     -18.212  69.611   4.399  1.00  0.00
ATOM   1422  C   LYS   318     -17.013  70.417   3.856  1.00  0.00
ATOM   1423  O   LYS   318     -17.260  71.397   3.145  1.00  0.00
ATOM   1424  CB  LYS   318     -18.793  70.127   5.719  1.00  0.00
ATOM   1425  CG  LYS   318     -20.231  69.906   6.149  1.00  0.00
ATOM   1426  CD  LYS   318     -21.217  70.408   5.102  1.00  0.00
ATOM   1427  CE  LYS   318     -22.546  69.563   5.059  1.00  0.00
ATOM   1428  NZ  LYS   318     -22.944  69.377   6.519  1.00  0.00
ATOM   1429  N   GLY   319     -15.797  70.117   4.311  1.00  0.00
ATOM   1430  CA  GLY   319     -14.580  70.717   3.828  1.00  0.00
ATOM   1431  C   GLY   319     -14.198  70.017   2.505  1.00  0.00
ATOM   1432  O   GLY   319     -13.423  70.558   1.720  1.00  0.00
ATOM   1433  OXT GLY   319     -14.922  69.078   2.091  1.00  0.00
TER
END
