
#######################################################
#                                                     #
#                        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    4 (   32),  selected    4 , name T0298TS319_3-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS319_3-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:     4       316 - 319         0.40     0.40
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.40     0.40
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.40     0.40
  LCS_AVERAGE:      2.70

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     V     316     V     316      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     R     317     R     317      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     K     318     K     318      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     G     319     G     319      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   2.70  (   2.70    2.70    2.70 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   2.03   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70
GDT RMS_LOCAL    0.11   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40
GDT RMS_ALL_CA   0.50   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.269
LGA    R     317      R     317          0.292
LGA    K     318      K     318          0.280
LGA    G     319      G     319          0.634

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.40     2.703     2.703     0.801

LGA_LOCAL      RMSD =  0.400  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.399  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.400  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.883766 * X  +  -0.466159 * Y  +  -0.040670 * Z  + -38.778507
  Y_new =  -0.132613 * X  +  -0.332866 * Y  +   0.933603 * Z  +  76.752869
  Z_new =  -0.448745 * X  +  -0.819693 * Y  +  -0.355995 * Z  +  59.946335 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.980520    1.161073  [ DEG:  -113.4754     66.5246 ]
  Theta =   0.465360    2.676232  [ DEG:    26.6632    153.3368 ]
  Phi   =  -0.148943    2.992649  [ DEG:    -8.5338    171.4662 ]
 
# 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: T0298TS319_3-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS319_3-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4  148   4.0    4   0.40   2.703     0.40
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS319_3-D1
PFRMAT TS
TARGET T0298
MODEL 3
PARENT N/A
ATOM   1395  N   VAL   316     -13.532  65.860   4.233  1.00111.74       1SG1396
ATOM   1396  CA  VAL   316     -14.174  65.485   3.013  1.00111.74       1SG1397
ATOM   1397  CB  VAL   316     -14.005  64.024   2.693  1.00111.74       1SG1398
ATOM   1398  CG1 VAL   316     -12.508  63.755   2.450  1.00111.74       1SG1399
ATOM   1399  CG2 VAL   316     -14.596  63.179   3.834  1.00111.74       1SG1400
ATOM   1400  C   VAL   316     -15.637  65.818   3.046  1.00111.74       1SG1401
ATOM   1401  O   VAL   316     -16.133  66.505   2.154  1.00111.74       1SG1402
ATOM   1402  N   ARG   317     -16.378  65.355   4.073  1.00108.46       1SG1403
ATOM   1403  CA  ARG   317     -17.800  65.558   3.999  1.00108.46       1SG1404
ATOM   1404  CB  ARG   317     -18.565  64.825   5.115  1.00108.46       1SG1405
ATOM   1405  CG  ARG   317     -18.319  63.316   5.134  1.00108.46       1SG1406
ATOM   1406  CD  ARG   317     -18.508  62.634   3.777  1.00108.46       1SG1407
ATOM   1407  NE  ARG   317     -18.219  61.182   3.963  1.00108.46       1SG1408
ATOM   1408  CZ  ARG   317     -17.654  60.466   2.948  1.00108.46       1SG1409
ATOM   1409  NH1 ARG   317     -17.369  61.085   1.765  1.00108.46       1SG1410
ATOM   1410  NH2 ARG   317     -17.361  59.142   3.113  1.00108.46       1SG1411
ATOM   1411  C   ARG   317     -18.195  67.001   4.090  1.00108.46       1SG1412
ATOM   1412  O   ARG   317     -18.700  67.579   3.130  1.00108.46       1SG1413
ATOM   1413  N   LYS   318     -17.937  67.627   5.256  1.00143.49       1SG1414
ATOM   1414  CA  LYS   318     -18.359  68.977   5.508  1.00143.49       1SG1415
ATOM   1415  CB  LYS   318     -18.179  69.384   6.983  1.00143.49       1SG1416
ATOM   1416  CG  LYS   318     -19.082  68.624   7.960  1.00143.49       1SG1417
ATOM   1417  CD  LYS   318     -20.579  68.850   7.726  1.00143.49       1SG1418
ATOM   1418  CE  LYS   318     -21.224  67.807   6.814  1.00143.49       1SG1419
ATOM   1419  NZ  LYS   318     -21.393  66.532   7.549  1.00143.49       1SG1420
ATOM   1420  C   LYS   318     -17.545  69.922   4.693  1.00143.49       1SG1421
ATOM   1421  O   LYS   318     -18.071  70.850   4.081  1.00143.49       1SG1422
ATOM   1422  N   GLY   319     -16.221  69.694   4.660  1.00 25.51       1SG1423
ATOM   1423  CA  GLY   319     -15.358  70.599   3.968  1.00 25.51       1SG1424
ATOM   1424  C   GLY   319     -15.450  70.296   2.483  1.00 25.51       1SG1425
ATOM   1425  O   GLY   319     -16.116  69.290   2.130  1.00 25.51       1SG1426
ATOM   1426  OXT GLY   319     -14.855  71.067   1.681  1.00 25.51       1SG1427
TER
END
