
#######################################################
#                                                     #
#                        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 (   36),  selected    5 , name T0316TS464_1-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    5 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_1-D1.T0316_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       189 - 193         1.47     1.47
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       189 - 193         1.47     1.47
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       189 - 192         0.66     2.00
  LCS_AVERAGE:      2.02

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:  188
LCS_GDT     S     189     S     189      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     190     T     190      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     191     A     191      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     192     K     192      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     193     K     193      3    5    5     3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.45  (   2.02    2.66    2.66 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.60   2.13   2.13   2.13   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66
GDT RMS_LOCAL    0.08   0.66   0.66   0.66   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47
GDT RMS_ALL_CA   2.33   2.00   2.00   2.00   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47

#      Molecule1      Molecule2       DISTANCE
LGA    S     189      S     189          0.807
LGA    T     190      T     190          1.386
LGA    A     191      A     191          0.588
LGA    K     192      K     192          1.762
LGA    K     193      K     193          2.183

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  188    4.0      5    1.47     2.394     2.541     0.319

LGA_LOCAL      RMSD =  1.469  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.469  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.469  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.373384 * X  +   0.821865 * Y  +   0.430258 * Z  + -25.118618
  Y_new =   0.311552 * X  +  -0.547958 * Y  +   0.776323 * Z  +  44.977505
  Z_new =   0.873796 * X  +  -0.155818 * Y  +  -0.460653 * Z  +   9.995744 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.815419    0.326174  [ DEG:  -161.3116     18.6884 ]
  Theta =  -1.062955   -2.078638  [ DEG:   -60.9028   -119.0972 ]
  Phi   =   0.695369   -2.446224  [ DEG:    39.8417   -140.1583 ]
 
# 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: T0316TS464_1-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_1-D1.T0316_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  188   4.0    5   1.47   2.541     1.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_1-D1
PFRMAT TS
TARGET T0316
MODEL 1
PARENT N/A
ATOM    753  N   SER   189      22.866  49.165  14.028  1.00  0.00
ATOM    754  CA  SER   189      23.734  49.504  12.945  1.00  0.00
ATOM    755  CB  SER   189      25.016  50.220  13.403  1.00  0.00
ATOM    756  OG  SER   189      25.831  50.528  12.283  1.00  0.00
ATOM    757  C   SER   189      24.131  48.204  12.348  1.00  0.00
ATOM    758  O   SER   189      24.467  48.124  11.168  1.00  0.00
ATOM    759  N   THR   190      24.081  47.135  13.168  1.00  0.00
ATOM    760  CA  THR   190      24.437  45.859  12.644  1.00  0.00
ATOM    761  CB  THR   190      24.321  44.738  13.638  1.00  0.00
ATOM    762  OG1 THR   190      23.000  44.668  14.152  1.00  0.00
ATOM    763  CG2 THR   190      25.342  44.953  14.766  1.00  0.00
ATOM    764  C   THR   190      23.511  45.574  11.517  1.00  0.00
ATOM    765  O   THR   190      23.954  45.174  10.442  1.00  0.00
ATOM    766  N   ALA   191      22.194  45.775  11.724  1.00  0.00
ATOM    767  CA  ALA   191      21.359  45.610  10.577  1.00  0.00
ATOM    768  CB  ALA   191      19.866  45.851  10.849  1.00  0.00
ATOM    769  C   ALA   191      21.812  46.705   9.688  1.00  0.00
ATOM    770  O   ALA   191      21.663  47.889   9.980  1.00  0.00
ATOM    771  N   LYS   192      22.408  46.294   8.572  1.00  0.00
ATOM    772  CA  LYS   192      22.922  47.165   7.578  1.00  0.00
ATOM    773  CB  LYS   192      24.419  47.487   7.768  1.00  0.00
ATOM    774  CG  LYS   192      25.310  46.267   8.021  1.00  0.00
ATOM    775  CD  LYS   192      26.807  46.573   7.932  1.00  0.00
ATOM    776  CE  LYS   192      27.305  46.797   6.503  1.00  0.00
ATOM    777  NZ  LYS   192      26.861  48.120   6.011  1.00  0.00
ATOM    778  C   LYS   192      22.727  46.337   6.369  1.00  0.00
ATOM    779  O   LYS   192      21.597  45.974   6.042  1.00  0.00
ATOM    780  N   LYS   193      23.807  46.005   5.652  1.00  0.00
ATOM    781  CA  LYS   193      23.541  45.112   4.581  1.00  0.00
ATOM    782  CB  LYS   193      24.659  45.069   3.528  1.00  0.00
ATOM    783  CG  LYS   193      24.847  46.413   2.826  1.00  0.00
ATOM    784  CD  LYS   193      23.565  46.923   2.167  1.00  0.00
ATOM    785  CE  LYS   193      22.560  47.514   3.158  1.00  0.00
ATOM    786  NZ  LYS   193      23.004  48.862   3.582  1.00  0.00
ATOM    787  C   LYS   193      23.429  43.755   5.191  1.00  0.00
ATOM    788  O   LYS   193      24.430  43.079   5.423  1.00  0.00
TER
END
