
#######################################################
#                                                     #
#                        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 (   41),  selected    5 , name T0316TS276_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected    5 , name T0316_D3.pdb
# PARAMETERS: T0316TS276_2-D3.T0316_D3.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       284 - 288         1.68     1.68
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       284 - 288         1.68     1.68
  LCS_AVERAGE:      5.56

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       284 - 286         0.75     6.25
  LONGEST_CONTINUOUS_SEGMENT:     3       285 - 287         0.01     3.10
  LONGEST_CONTINUOUS_SEGMENT:     3       286 - 288         0.11     6.27
  LCS_AVERAGE:      3.33

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:   90
LCS_GDT     M     284     M     284      3    5    5     0    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     285     S     285      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     286     T     286      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     287     S     287      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     288     L     288      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   4.81  (   3.33    5.56    5.56 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   3.33   3.33   4.44   4.44   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56
GDT RMS_LOCAL    0.01   0.01   1.09   1.09   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68
GDT RMS_ALL_CA   3.10   3.10   2.74   2.74   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68   1.68

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284          1.680
LGA    S     285      S     285          2.490
LGA    T     286      T     286          0.590
LGA    S     287      S     287          1.895
LGA    L     288      L     288          1.077

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   90    4.0      5    1.68     4.722     5.219     0.281

LGA_LOCAL      RMSD =  1.680  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.680  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.680  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.369420 * X  +  -0.909916 * Y  +  -0.188631 * Z  +  51.700035
  Y_new =  -0.926135 * X  +  -0.343871 * Y  +  -0.155007 * Z  +  66.972260
  Z_new =   0.076179 * X  +   0.231960 * Y  +  -0.969738 * Z  +  33.679192 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.906805   -0.234788  [ DEG:   166.5477    -13.4523 ]
  Theta =  -0.076253   -3.065340  [ DEG:    -4.3690   -175.6310 ]
  Phi   =  -1.191252    1.950340  [ DEG:   -68.2537    111.7463 ]
 
# 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: T0316TS276_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS276_2-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   90   4.0    5   1.68   5.219     1.68
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS276_2-D3
PFRMAT TS 
TARGET T0316
MODEL 2
PARENT 1K92_A
ATOM   5133  H   MET   284      23.218  11.032 -15.826  1.00  0.00               
ATOM   5135  N   MET   284      23.713  10.251 -15.638  1.00  0.00               
ATOM   5137  CA  MET   284      24.658  10.315 -14.509  1.00  0.00               
ATOM   5139  CB  MET   284      25.299  11.675 -14.399  1.00  0.00               
ATOM   5141  C   MET   284      24.094   9.872 -13.172  1.00  0.00               
ATOM   5143  O   MET   284      24.843   9.526 -12.267  1.00  0.00               
ATOM   5145  CG  MET   284      26.361  11.739 -13.320  1.00  0.00               
ATOM   5147  SD  MET   284      27.219  13.324 -13.296  1.00  0.00               
ATOM   5149  CE  MET   284      28.270  13.145 -14.731  1.00  0.00               
ATOM   5151  H   SER   285      22.247  10.078 -13.775  1.00  0.00               
ATOM   5153  N   SER   285      22.794   9.969 -13.027  1.00  0.00               
ATOM   5155  CA  SER   285      22.159   9.882 -11.716  1.00  0.00               
ATOM   5157  CB  SER   285      20.671  10.082 -11.838  1.00  0.00               
ATOM   5159  C   SER   285      22.441   8.626 -10.905  1.00  0.00               
ATOM   5161  O   SER   285      22.281   8.674  -9.683  1.00  0.00               
ATOM   5163  OG  SER   285      20.052   9.876 -10.587  1.00  0.00               
ATOM   5165  H   THR   286      22.817   7.394 -12.411  1.00  0.00               
ATOM   5167  N   THR   286      22.836   7.511 -11.481  1.00  0.00               
ATOM   5169  CA  THR   286      23.228   6.432 -10.594  1.00  0.00               
ATOM   5171  CB  THR   286      23.317   5.095 -11.359  1.00  0.00               
ATOM   5173  C   THR   286      24.606   6.794 -10.033  1.00  0.00               
ATOM   5175  O   THR   286      25.536   7.079 -10.789  1.00  0.00               
ATOM   5177  CG2 THR   286      21.979   4.735 -11.993  1.00  0.00               
ATOM   5179  OG1 THR   286      24.303   5.221 -12.388  1.00  0.00               
ATOM   5181  H   SER   287      24.096   6.319  -8.192  1.00  0.00               
ATOM   5183  N   SER   287      24.769   6.686  -8.723  1.00  0.00               
ATOM   5185  CA  SER   287      25.982   7.188  -8.079  1.00  0.00               
ATOM   5187  CB  SER   287      25.940   8.724  -7.964  1.00  0.00               
ATOM   5189  C   SER   287      26.265   6.539  -6.729  1.00  0.00               
ATOM   5191  O   SER   287      25.432   5.798  -6.201  1.00  0.00               
ATOM   5193  OG  SER   287      24.853   9.152  -7.152  1.00  0.00               
ATOM   5195  H   LEU   288      28.025   7.428  -6.603  1.00  0.00               
ATOM   5197  N   LEU   288      27.417   6.866  -6.144  1.00  0.00               
ATOM   5199  CA  LEU   288      27.745   6.421  -4.791  1.00  0.00               
ATOM   5201  CB  LEU   288      29.151   5.821  -4.756  1.00  0.00               
ATOM   5203  C   LEU   288      27.657   7.570  -3.788  1.00  0.00               
ATOM   5205  O   LEU   288      26.552   8.127  -3.624  1.00  0.00               
ATOM   5207  OXT LEU   288      28.720   8.005  -3.298  1.00  0.00               
ATOM   5209  CG  LEU   288      29.335   4.481  -5.461  1.00  0.00               
ATOM   5211  CD1 LEU   288      30.810   4.109  -5.489  1.00  0.00               
ATOM   5213  CD2 LEU   288      28.530   3.402  -4.747  1.00  0.00               
TER 
END
