
#######################################################
#                                                     #
#                        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 T0298TS671_4-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS671_4-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         0.29     0.29
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.29     0.29
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.29     0.29
  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     4    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     4    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     4    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     4    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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   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   2.70
GDT RMS_LOCAL    0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29
GDT RMS_ALL_CA   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29   0.29

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.216
LGA    R     317      R     317          0.237
LGA    K     318      K     318          0.369
LGA    G     319      G     319          0.322

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.29     2.703     2.703     1.018

LGA_LOCAL      RMSD =  0.293  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.293  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.293  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.626871 * X  +   0.324710 * Y  +   0.708234 * Z  + -33.775299
  Y_new =  -0.506946 * X  +  -0.860266 * Y  +  -0.054294 * Z  + 109.314621
  Z_new =   0.591640 * X  +  -0.393072 * Y  +   0.703887 * Z  +   6.274772 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.509293    2.632300  [ DEG:   -29.1803    150.8197 ]
  Theta =  -0.633092   -2.508501  [ DEG:   -36.2735   -143.7265 ]
  Phi   =  -2.461575    0.680018  [ DEG:  -141.0378     38.9622 ]
 
# 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_4-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS671_4-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   0.29   2.703     0.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS671_4-D1
PFRMAT TS
TARGET T0298
MODEL  4  REFINED
PARENT 1GL3_A 1BRM_C 1MB4_B 1PQU_D
ATOM   1395  N   VAL   316     -13.385  65.769   3.961  1.00  0.00
ATOM   1396  CA  VAL   316     -14.105  65.229   2.847  1.00  0.00
ATOM   1397  C   VAL   316     -15.650  65.590   2.912  1.00  0.00
ATOM   1398  O   VAL   316     -16.162  66.274   2.008  1.00  0.00
ATOM   1399  CB  VAL   316     -13.856  63.753   2.770  1.00  0.00
ATOM   1400  CG1 VAL   316     -14.584  63.108   1.591  1.00  0.00
ATOM   1401  CG2 VAL   316     -12.363  63.465   2.549  1.00  0.00
ATOM   1402  N   ARG   317     -16.331  65.233   4.042  1.00  0.00
ATOM   1403  CA  ARG   317     -17.794  65.441   4.158  1.00  0.00
ATOM   1404  C   ARG   317     -18.244  66.906   4.191  1.00  0.00
ATOM   1405  O   ARG   317     -18.690  67.348   3.143  1.00  0.00
ATOM   1406  CB  ARG   317     -18.360  64.531   5.283  1.00  0.00
ATOM   1407  CG  ARG   317     -18.367  63.024   4.905  1.00  0.00
ATOM   1408  CD  ARG   317     -18.937  62.364   6.140  1.00  0.00
ATOM   1409  NE  ARG   317     -19.003  60.895   5.866  1.00  0.00
ATOM   1410  CZ  ARG   317     -20.161  60.402   5.426  1.00  0.00
ATOM   1411  NH1 ARG   317     -21.209  61.213   5.135  1.00  0.00
ATOM   1412  NH2 ARG   317     -20.352  59.036   5.425  1.00  0.00
ATOM   1413  N   LYS   318     -17.955  67.646   5.263  1.00  0.00
ATOM   1414  CA  LYS   318     -18.475  69.043   5.373  1.00  0.00
ATOM   1415  C   LYS   318     -17.582  70.091   4.639  1.00  0.00
ATOM   1416  O   LYS   318     -18.157  70.939   3.951  1.00  0.00
ATOM   1417  CB  LYS   318     -18.617  69.382   6.872  1.00  0.00
ATOM   1418  CG  LYS   318     -19.839  68.917   7.686  1.00  0.00
ATOM   1419  CD  LYS   318     -21.139  69.401   7.056  1.00  0.00
ATOM   1420  CE  LYS   318     -22.345  68.416   7.308  1.00  0.00
ATOM   1421  NZ  LYS   318     -22.252  68.048   8.784  1.00  0.00
ATOM   1422  N   GLY   319     -16.251  70.052   4.798  1.00  0.00
ATOM   1423  CA  GLY   319     -15.317  70.905   4.109  1.00  0.00
ATOM   1424  C   GLY   319     -15.109  70.340   2.677  1.00  0.00
ATOM   1425  O   GLY   319     -14.400  70.950   1.866  1.00  0.00
ATOM   1426  OXT GLY   319     -15.572  69.240   2.409  1.00  0.00
TER
END
