
#######################################################
#                                                     #
#                        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 (    5),  selected    5 , name T0320TS464_4_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected    5 , name T0320_D2.pdb
# PARAMETERS: T0320TS464_4_2-D2.T0320_D2.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       272 - 276         3.06     3.06
  LCS_AVERAGE:      6.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       272 - 275         1.11     4.00
  LCS_AVERAGE:      5.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       272 - 274         0.40     4.87
  LONGEST_CONTINUOUS_SEGMENT:     3       273 - 275         0.67     3.79
  LONGEST_CONTINUOUS_SEGMENT:     3       274 - 276         0.47     6.36
  LCS_AVERAGE:      4.11

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:   73
LCS_GDT     I     272     I     272      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     273     S     273      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     274     V     274      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     275     V     275      3    4    5     1    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     276     D     276      3    3    5     0    3    3    3    3    3    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.39  (   4.11    5.21    6.85 )

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      3      4      4      4      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   4.11   4.11   5.48   5.48   5.48   5.48   5.48   5.48   5.48   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85
GDT RMS_LOCAL    0.40   0.40   1.11   1.11   1.11   1.11   1.11   1.11   1.11   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06
GDT RMS_ALL_CA   4.87   4.87   4.00   4.00   4.00   4.00   4.00   4.00   4.00   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06

#      Molecule1      Molecule2       DISTANCE
LGA    I     272      I     272          1.203
LGA    S     273      S     273          0.890
LGA    V     274      V     274          0.829
LGA    V     275      V     275          1.423
LGA    D     276      D     276          8.662

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   73    4.0      4    1.11     5.479     5.633     0.330

LGA_LOCAL      RMSD =  1.113  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.999  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  3.063  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.664820 * X  +   0.215698 * Y  +   0.715184 * Z  + -26.571253
  Y_new =   0.709409 * X  +   0.117594 * Y  +  -0.694918 * Z  + -26.761074
  Z_new =  -0.233993 * X  +   0.969353 * Y  +  -0.074839 * Z  + -62.007038 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.647849   -1.493744  [ DEG:    94.4148    -85.5852 ]
  Theta =   0.236183    2.905410  [ DEG:    13.5323    166.4677 ]
  Phi   =   0.817833   -2.323760  [ DEG:    46.8584   -133.1416 ]
 
# 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: T0320TS464_4_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_2-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   73   4.0    4   1.11   5.633     3.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM     29  CA  ILE   272      15.912  31.914   3.814  1.00  0.00
ATOM     30  CA  SER   273      19.536  32.805   3.011  1.00  0.00
ATOM     31  CA  VAL   274      21.583  33.552  -0.110  1.00  0.00
ATOM     32  CA  VAL   275      25.362  33.342  -0.352  1.00  0.00
ATOM     33  CA  ASP   276      26.698  35.183  -3.398  1.00  0.00
TER
END
