
#######################################################
#                                                     #
#                        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 (   76),  selected    5 , name T0301TS069_1-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected    5 , name T0301_D1.pdb
# PARAMETERS: T0301TS069_1-D1.T0301_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       178 - 182         1.78     1.78
  LCS_AVERAGE:      2.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       178 - 182         1.78     1.78
  LCS_AVERAGE:      2.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       178 - 181         0.26     2.47
  LCS_AVERAGE:      1.90

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:  200
LCS_GDT     F     178     F     178      4    5    5     4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     179     L     179      4    5    5     4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     180     D     180      4    5    5     4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     P     181     P     181      4    5    5     4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     182     S     182      3    5    5     0    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.30  (   1.90    2.50    2.50 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   2.00   2.00   2.00   2.00   2.00   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50
GDT RMS_LOCAL    0.26   0.26   0.26   0.26   0.26   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78
GDT RMS_ALL_CA   2.47   2.47   2.47   2.47   2.47   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78

#      Molecule1      Molecule2       DISTANCE
LGA    F     178      F     178          1.100
LGA    L     179      L     179          1.299
LGA    D     180      D     180          0.561
LGA    P     181      P     181          1.945
LGA    S     182      S     182          2.982

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  200    4.0      5    1.78     2.250     2.355     0.266

LGA_LOCAL      RMSD =  1.782  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.782  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.782  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.794413 * X  +  -0.200117 * Y  +   0.573464 * Z  +  83.179993
  Y_new =  -0.578366 * X  +  -0.039079 * Y  +  -0.814841 * Z  +  -2.009039
  Z_new =   0.185474 * X  +  -0.978992 * Y  +  -0.084696 * Z  +  20.835192 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.657095    1.484498  [ DEG:   -94.9445     85.0555 ]
  Theta =  -0.186554   -2.955038  [ DEG:   -10.6888   -169.3112 ]
  Phi   =  -2.512293    0.629299  [ DEG:  -143.9438     36.0562 ]
 
# 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: T0301TS069_1-D1                               
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS069_1-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  200   4.0    5   1.78   2.355     1.78
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS069_1-D1
PFRMAT TS
TARGET T0301
MODEL 1
PARENT 1O9J_D
ATOM      1  N   PHE   178      78.523  11.966   7.303  1.00 10.00
ATOM      2  CA  PHE   178      79.536  11.172   6.730  1.00 10.00
ATOM      3  C   PHE   178      78.962   9.956   6.009  1.00 10.00
ATOM      4  O   PHE   178      78.284   9.078   6.664  1.00 10.00
ATOM      5  CB  PHE   178      80.510  10.793   7.853  1.00 10.00
ATOM      6  CG  PHE   178      81.664   9.956   7.364  1.00 10.00
ATOM      7  CD1 PHE   178      82.837  10.581   6.899  1.00 10.00
ATOM      8  CD2 PHE   178      81.646   8.557   7.524  1.00 10.00
ATOM      9  CE1 PHE   178      83.961   9.813   6.560  1.00 10.00
ATOM     10  CE2 PHE   178      82.772   7.789   7.187  1.00 10.00
ATOM     11  CZ  PHE   178      83.932   8.419   6.713  1.00 10.00
ATOM     12 HN   PHE   178      78.783  12.808   7.763  1.00 10.00
ATOM     13 HA   PHE   178      80.075  11.800   5.983  1.00 10.00
ATOM     14 HB1  PHE   178      80.910  11.730   8.308  1.00 10.00
ATOM     15 HB2  PHE   178      79.955  10.253   8.655  1.00 10.00
ATOM     16 HD1  PHE   178      82.880  11.667   6.787  1.00 10.00
ATOM     17 HD2  PHE   178      80.751   8.066   7.903  1.00 10.00
ATOM     18 HE1  PHE   178      84.854  10.310   6.182  1.00 10.00
ATOM     19 HE2  PHE   178      82.746   6.708   7.301  1.00 10.00
ATOM     20 HZ   PHE   178      84.811   7.831   6.454  1.00 10.00
ATOM     21  N   LEU   179      79.175   9.795   4.691  1.00 10.00
ATOM     22  CA  LEU   179      78.475   8.872   3.855  1.00 10.00
ATOM     23  C   LEU   179      79.323   8.396   2.681  1.00 10.00
ATOM     24  O   LEU   179      79.804   9.225   1.833  1.00 10.00
ATOM     25  CB  LEU   179      77.199   9.527   3.292  1.00 10.00
ATOM     26  CG  LEU   179      76.126   9.923   4.324  1.00 10.00
ATOM     27  CD1 LEU   179      75.126  10.870   3.678  1.00 10.00
ATOM     28 HN   LEU   179      80.072  10.105   4.394  1.00 10.00
ATOM     29 HA   LEU   179      78.203   7.958   4.430  1.00 10.00
ATOM     30 HB1  LEU   179      77.524  10.442   2.736  1.00 10.00
ATOM     31 HB2  LEU   179      76.727   8.845   2.544  1.00 10.00
ATOM     32  CD2 LEU   179      75.394   8.715   4.931  1.00 10.00
ATOM     33 HG   LEU   179      76.590  10.506   5.148  1.00 10.00
ATOM     34 HD11 LEU   179      75.631  11.722   3.180  1.00 10.00
ATOM     35 HD12 LEU   179      74.492  11.284   4.486  1.00 10.00
ATOM     36 HD13 LEU   179      74.510  10.346   2.913  1.00 10.00
ATOM     37 HD21 LEU   179      74.624   9.060   5.658  1.00 10.00
ATOM     38 HD22 LEU   179      76.103   8.056   5.477  1.00 10.00
ATOM     39 HD23 LEU   179      74.891   8.120   4.134  1.00 10.00
ATOM     40  N   ASP   180      79.562   7.082   2.555  1.00 10.00
ATOM     41  CA  ASP   180      80.436   6.477   1.616  1.00 10.00
ATOM     42  C   ASP   180      81.847   7.130   1.621  1.00 10.00
ATOM     43  O   ASP   180      82.358   7.618   0.547  1.00 10.00
ATOM     44  CB  ASP   180      79.720   6.389   0.242  1.00 10.00
ATOM     45  CG  ASP   180      80.164   5.237  -0.618  1.00 10.00
ATOM     46  OD1 ASP   180      80.203   5.361  -1.918  1.00 10.00
ATOM     47 HN   ASP   180      79.223   6.514   3.288  1.00 10.00
ATOM     48 HA   ASP   180      80.537   5.429   1.970  1.00 10.00
ATOM     49 HB1  ASP   180      79.861   7.338  -0.324  1.00 10.00
ATOM     50 HB2  ASP   180      78.626   6.240   0.381  1.00 10.00
ATOM     51  OD2 ASP   180      80.640   4.144  -0.068  1.00 10.00
ATOM     52  N   PRO   181      82.572   7.163   2.780  1.00 10.00
ATOM     53  CA  PRO   181      83.838   7.928   2.914  1.00 10.00
ATOM     54  C   PRO   181      83.992   9.326   2.337  1.00 10.00
ATOM     55  O   PRO   181      85.162   9.847   2.391  1.00 10.00
ATOM     56  CB  PRO   181      84.846   6.873   2.484  1.00 10.00
ATOM     57 HA   PRO   181      84.045   8.124   3.995  1.00 10.00
ATOM     58 HB1  PRO   181      84.742   6.636   1.398  1.00 10.00
ATOM     59 HB2  PRO   181      85.893   7.179   2.710  1.00 10.00
ATOM     60  CG  PRO   181      84.389   5.710   3.368  1.00 10.00
ATOM     61 HG1  PRO   181      84.698   4.734   2.928  1.00 10.00
ATOM     62 HG2  PRO   181      84.824   5.806   4.391  1.00 10.00
ATOM     63  CD  PRO   181      82.865   5.868   3.435  1.00 10.00
ATOM     64 HD1  PRO   181      82.456   5.853   4.472  1.00 10.00
ATOM     65 HD2  PRO   181      82.456   4.992   2.879  1.00 10.00
ATOM     66  N   SER   182      82.922  10.118   2.120  1.00 10.00
ATOM     67  CA  SER   182      83.032  11.545   1.967  1.00 10.00
ATOM     68  C   SER   182      82.078  12.365   2.833  1.00 10.00
ATOM     69  O   SER   182      81.230  11.763   3.589  1.00 10.00
ATOM     70  CB  SER   182      82.798  11.855   0.482  1.00 10.00
ATOM     71 HN   SER   182      82.153   9.823   2.673  1.00 10.00
ATOM     72 HA   SER   182      84.035  11.912   2.286  1.00 10.00
ATOM     73 HB1  SER   182      81.757  11.553   0.204  1.00 10.00
ATOM     74 HB2  SER   182      83.503  11.249  -0.132  1.00 10.00
ATOM     75  OG  SER   182      82.999  13.254   0.185  1.00 10.00
ATOM     76 HG   SER   182      82.119  13.722   0.489  1.00 10.00
TER
END
