
#######################################################
#                                                     #
#                        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 (   40),  selected    5 , name T0316TS277_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected    5 , name T0316_D3.pdb
# PARAMETERS: T0316TS277_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         1.06     1.06
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       284 - 288         1.06     1.06
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       284 - 287         0.89     1.85
  LONGEST_CONTINUOUS_SEGMENT:     4       285 - 288         0.88     1.51
  LCS_AVERAGE:      4.44

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      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     285     S     285      4    5    5     0    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     286     T     286      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     287     S     287      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     288     L     288      4    5    5     3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.19  (   4.44    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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   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   5.56
GDT RMS_LOCAL    0.28   0.89   0.75   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06
GDT RMS_ALL_CA   1.23   1.85   1.24   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284          0.892
LGA    S     285      S     285          1.341
LGA    T     286      T     286          1.507
LGA    S     287      S     287          0.318
LGA    L     288      L     288          0.829

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   90    4.0      5    1.06     5.278     5.385     0.430

LGA_LOCAL      RMSD =  1.063  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.063  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.063  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.538614 * X  +   0.303128 * Y  +  -0.786135 * Z  +  79.516624
  Y_new =   0.271752 * X  +   0.945676 * Y  +   0.178458 * Z  + -43.311069
  Z_new =   0.797525 * X  +  -0.117514 * Y  +  -0.591730 * Z  +  -7.128797 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.945550    0.196043  [ DEG:  -168.7676     11.2324 ]
  Theta =  -0.923181   -2.218411  [ DEG:   -52.8944   -127.1056 ]
  Phi   =   2.674320   -0.467272  [ DEG:   153.2273    -26.7727 ]
 
# 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: T0316TS277_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS277_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   1.06   5.385     1.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS277_2-D3
PFRMAT TS 
TARGET T0316
MODEL 2
PARENT 1K92_A
ATOM   5135  H   MET   284      21.066  10.929 -15.654  1.00  0.00                              
ATOM   5137  N   MET   284      21.932  11.295 -15.743  1.00  0.00                              
ATOM   5139  CA  MET   284      22.800  11.392 -14.573  1.00  0.00                              
ATOM   5141  CB  MET   284      22.173  12.210 -13.466  1.00  0.00                              
ATOM   5143  C   MET   284      23.184  10.049 -14.043  1.00  0.00                              
ATOM   5145  O   MET   284      22.326   9.183 -13.827  1.00  0.00                              
ATOM   5147  CG  MET   284      23.039  12.256 -12.203  1.00  0.00                              
ATOM   5149  SD  MET   284      24.605  13.124 -12.468  1.00  0.00                              
ATOM   5151  CE  MET   284      24.136  14.797 -12.054  1.00  0.00                              
ATOM   5153  H   SER   285      25.075  10.505 -14.074  1.00  0.00                              
ATOM   5155  N   SER   285      24.458   9.851 -13.847  1.00  0.00                              
ATOM   5157  CA  SER   285      24.924   8.646 -13.270  1.00  0.00                              
ATOM   5159  CB  SER   285      26.431   8.495 -13.510  1.00  0.00                              
ATOM   5161  C   SER   285      24.619   8.639 -11.777  1.00  0.00                              
ATOM   5163  O   SER   285      25.102   9.488 -11.025  1.00  0.00                              
ATOM   5165  OG  SER   285      26.895   7.254 -12.997  1.00  0.00                              
ATOM   5167  H   THR   286      23.371   7.186 -11.990  1.00  0.00                              
ATOM   5169  N   THR   286      23.783   7.741 -11.370  1.00  0.00                              
ATOM   5171  CA  THR   286      23.427   7.626  -9.981  1.00  0.00                              
ATOM   5173  CB  THR   286      22.061   6.947  -9.831  1.00  0.00                              
ATOM   5175  C   THR   286      24.480   6.845  -9.211  1.00  0.00                              
ATOM   5177  O   THR   286      25.603   6.660  -9.699  1.00  0.00                              
ATOM   5179  CG2 THR   286      20.939   7.894 -10.256  1.00  0.00                              
ATOM   5181  OG1 THR   286      22.026   5.779 -10.657  1.00  0.00                              
ATOM   5183  H   SER   287      23.331   6.704  -7.602  1.00  0.00                              
ATOM   5185  N   SER   287      24.147   6.435  -7.982  1.00  0.00                              
ATOM   5187  CA  SER   287      25.053   5.608  -7.178  1.00  0.00                              
ATOM   5189  CB  SER   287      26.204   5.064  -8.025  1.00  0.00                              
ATOM   5191  C   SER   287      25.604   6.364  -5.984  1.00  0.00                              
ATOM   5193  O   SER   287      24.850   6.950  -5.204  1.00  0.00                              
ATOM   5195  OG  SER   287      27.204   4.486  -7.192  1.00  0.00                              
ATOM   5197  H   LEU   288      27.446   5.877  -6.467  1.00  0.00                              
ATOM   5199  N   LEU   288      26.915   6.335  -5.829  1.00  0.00                              
ATOM   5201  CA  LEU   288      27.568   6.964  -4.687  1.00  0.00                              
ATOM   5203  CB  LEU   288      26.555   7.198  -3.563  1.00  0.00                              
ATOM   5205  C   LEU   288      28.694   6.099  -4.190  1.00  0.00                              
ATOM   5207  O   LEU   288      29.000   5.091  -4.803  1.00  0.00                              
ATOM   5209  CG  LEU   288      27.091   7.843  -2.283  1.00  0.00                              
ATOM   5211  CD1 LEU   288      27.690   9.209  -2.594  1.00  0.00                              
ATOM   5213  CD2 LEU   288      25.975   7.973  -1.256  1.00  0.00                              
TER 
END
