
#######################################################
#                                                     #
#                        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_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected    5 , name T0316_D3.pdb
# PARAMETERS: T0316TS276_1-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         1.74     1.74
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       284 - 288         1.74     1.74
  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         0.90     7.07
  LONGEST_CONTINUOUS_SEGMENT:     3       285 - 287         0.46     3.39
  LONGEST_CONTINUOUS_SEGMENT:     3       286 - 288         0.45     3.02
  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    4    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    4    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    4    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    4    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    4    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      4      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   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
GDT RMS_LOCAL    0.45   0.45   1.04   1.04   1.04   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74
GDT RMS_ALL_CA   3.02   3.02   2.26   2.26   2.26   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284          2.515
LGA    S     285      S     285          2.558
LGA    T     286      T     286          1.102
LGA    S     287      S     287          0.631
LGA    L     288      L     288          0.822

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   90    4.0      5    1.74     4.722     5.146     0.272

LGA_LOCAL      RMSD =  1.741  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.741  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.741  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.714896 * X  +  -0.694914 * Y  +  -0.077574 * Z  +  83.620453
  Y_new =  -0.605273 * X  +   0.670561 * Y  +  -0.428944 * Z  +  34.859589
  Z_new =   0.350097 * X  +  -0.259697 * Y  +  -0.899994 * Z  +  34.781834 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.860669    0.280923  [ DEG:  -163.9043     16.0957 ]
  Theta =  -0.357675   -2.783918  [ DEG:   -20.4933   -159.5067 ]
  Phi   =  -2.439042    0.702551  [ DEG:  -139.7468     40.2532 ]
 
# 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_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS276_1-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   1.74   5.146     1.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS276_1-D3
PFRMAT TS 
TARGET T0316
MODEL 1
PARENT 1K92_A
ATOM   5133  H   MET   284      25.268  10.656 -15.218  1.00  0.00               
ATOM   5135  N   MET   284      25.605  10.260 -14.424  1.00  0.00               
ATOM   5137  CA  MET   284      25.258  10.864 -13.111  1.00  0.00               
ATOM   5139  CB  MET   284      25.058  12.368 -13.239  1.00  0.00               
ATOM   5141  C   MET   284      24.094  10.184 -12.407  1.00  0.00               
ATOM   5143  O   MET   284      23.976  10.223 -11.179  1.00  0.00               
ATOM   5145  CG  MET   284      24.872  13.084 -11.914  1.00  0.00               
ATOM   5147  SD  MET   284      24.827  14.871 -12.128  1.00  0.00               
ATOM   5149  CE  MET   284      26.559  15.203 -12.456  1.00  0.00               
ATOM   5151  H   SER   285      23.434   9.571 -14.077  1.00  0.00               
ATOM   5153  N   SER   285      23.266   9.580 -13.187  1.00  0.00               
ATOM   5155  CA  SER   285      22.020   8.992 -12.714  1.00  0.00               
ATOM   5157  CB  SER   285      21.255   8.363 -13.882  1.00  0.00               
ATOM   5159  C   SER   285      22.262   7.947 -11.650  1.00  0.00               
ATOM   5161  O   SER   285      21.361   7.626 -10.871  1.00  0.00               
ATOM   5163  OG  SER   285      20.095   7.693 -13.417  1.00  0.00               
ATOM   5165  H   THR   286      24.148   7.755 -12.146  1.00  0.00               
ATOM   5167  N   THR   286      23.460   7.402 -11.617  1.00  0.00               
ATOM   5169  CA  THR   286      23.747   6.284 -10.746  1.00  0.00               
ATOM   5171  CB  THR   286      24.747   5.339 -11.432  1.00  0.00               
ATOM   5173  C   THR   286      24.359   6.788  -9.445  1.00  0.00               
ATOM   5175  O   THR   286      24.945   7.872  -9.407  1.00  0.00               
ATOM   5177  CG2 THR   286      24.986   4.094 -10.586  1.00  0.00               
ATOM   5179  OG1 THR   286      24.205   4.942 -12.696  1.00  0.00               
ATOM   5181  H   SER   287      23.893   5.136  -8.474  1.00  0.00               
ATOM   5183  N   SER   287      24.243   5.998  -8.383  1.00  0.00               
ATOM   5185  CA  SER   287      24.641   6.451  -7.053  1.00  0.00               
ATOM   5187  CB  SER   287      23.999   5.573  -5.977  1.00  0.00               
ATOM   5189  C   SER   287      26.147   6.444  -6.874  1.00  0.00               
ATOM   5191  O   SER   287      26.808   5.445  -7.153  1.00  0.00               
ATOM   5193  OG  SER   287      24.225   6.119  -4.689  1.00  0.00               
ATOM   5195  H   LEU   288      26.117   8.271  -6.132  1.00  0.00               
ATOM   5197  N   LEU   288      26.682   7.546  -6.355  1.00  0.00               
ATOM   5199  CA  LEU   288      28.106   7.646  -6.065  1.00  0.00               
ATOM   5201  CB  LEU   288      28.397   8.950  -5.312  1.00  0.00               
ATOM   5203  C   LEU   288      28.578   6.466  -5.226  1.00  0.00               
ATOM   5205  O   LEU   288      28.432   6.532  -3.990  1.00  0.00               
ATOM   5207  OXT LEU   288      28.900   5.414  -5.818  1.00  0.00               
ATOM   5209  CG  LEU   288      29.863   9.221  -4.951  1.00  0.00               
ATOM   5211  CD1 LEU   288      30.698   9.389  -6.212  1.00  0.00               
ATOM   5213  CD2 LEU   288      29.972  10.452  -4.066  1.00  0.00               
TER 
END
