
#######################################################
#                                                     #
#                        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_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected    5 , name T0316_D3.pdb
# PARAMETERS: T0316TS277_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         1.24     1.24
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       284 - 288         1.24     1.24
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       284 - 287         0.81     2.35
  LCS_AVERAGE:      4.22

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     3    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      3    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.11  (   4.22    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    0.27   0.68   0.68   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24
GDT RMS_ALL_CA   2.48   1.55   1.55   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284          1.060
LGA    S     285      S     285          1.197
LGA    T     286      T     286          1.829
LGA    S     287      S     287          0.711
LGA    L     288      L     288          1.107

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   90    4.0      5    1.24     5.278     5.385     0.374

LGA_LOCAL      RMSD =  1.235  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.235  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.235  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.603222 * X  +   0.161209 * Y  +  -0.781111 * Z  +  86.831314
  Y_new =   0.158936 * X  +   0.984014 * Y  +   0.080345 * Z  + -34.949566
  Z_new =   0.781577 * X  +  -0.075680 * Y  +  -0.619201 * Z  +  -6.085671 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.019973    0.121619  [ DEG:  -173.0317      6.9683 ]
  Theta =  -0.897189   -2.244403  [ DEG:   -51.4052   -128.5948 ]
  Phi   =   2.883970   -0.257623  [ DEG:   165.2393    -14.7607 ]
 
# 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_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS277_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   1.24   5.385     1.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS277_1-D3
PFRMAT TS 
TARGET T0316
MODEL 1
PARENT 1K92_A
ATOM   5135  H   MET   284      21.119  10.456 -15.981  1.00  0.00                              
ATOM   5137  N   MET   284      21.934  10.934 -15.986  1.00  0.00                              
ATOM   5139  CA  MET   284      22.662  11.148 -14.721  1.00  0.00                              
ATOM   5141  CB  MET   284      21.828  11.885 -13.699  1.00  0.00                              
ATOM   5143  C   MET   284      23.195   9.879 -14.103  1.00  0.00                              
ATOM   5145  O   MET   284      22.456   8.907 -13.894  1.00  0.00                              
ATOM   5147  CG  MET   284      22.525  11.993 -12.346  1.00  0.00                              
ATOM   5149  SD  MET   284      21.454  12.627 -11.056  1.00  0.00                              
ATOM   5151  CE  MET   284      21.191  14.284 -11.649  1.00  0.00                              
ATOM   5153  H   SER   285      24.987  10.655 -13.939  1.00  0.00                              
ATOM   5155  N   SER   285      24.460   9.900 -13.763  1.00  0.00                              
ATOM   5157  CA  SER   285      25.064   8.794 -13.092  1.00  0.00                              
ATOM   5159  CB  SER   285      26.580   8.851 -13.255  1.00  0.00                              
ATOM   5161  C   SER   285      24.731   8.856 -11.635  1.00  0.00                              
ATOM   5163  O   SER   285      25.231   9.751 -10.922  1.00  0.00                              
ATOM   5165  OG  SER   285      27.224   8.083 -12.250  1.00  0.00                              
ATOM   5167  H   THR   286      23.516   7.287 -11.751  1.00  0.00                              
ATOM   5169  N   THR   286      23.845   7.947 -11.172  1.00  0.00                              
ATOM   5171  CA  THR   286      23.398   7.941  -9.752  1.00  0.00                              
ATOM   5173  CB  THR   286      22.105   7.079  -9.576  1.00  0.00                              
ATOM   5175  C   THR   286      24.497   7.394  -8.834  1.00  0.00                              
ATOM   5177  O   THR   286      25.451   8.110  -8.497  1.00  0.00                              
ATOM   5179  CG2 THR   286      21.752   6.867  -8.091  1.00  0.00                              
ATOM   5181  OG1 THR   286      21.008   7.737 -10.231  1.00  0.00                              
ATOM   5183  H   SER   287      23.600   5.637  -8.659  1.00  0.00                              
ATOM   5185  N   SER   287      24.348   6.136  -8.401  1.00  0.00                              
ATOM   5187  CA  SER   287      25.355   5.494  -7.556  1.00  0.00                              
ATOM   5189  CB  SER   287      26.634   5.243  -8.356  1.00  0.00                              
ATOM   5191  C   SER   287      25.673   6.330  -6.315  1.00  0.00                              
ATOM   5193  O   SER   287      24.831   7.092  -5.835  1.00  0.00                              
ATOM   5195  OG  SER   287      27.629   4.688  -7.543  1.00  0.00                              
ATOM   5197  H   LEU   288      27.487   5.568  -6.199  1.00  0.00                              
ATOM   5199  N   LEU   288      26.881   6.163  -5.785  1.00  0.00                              
ATOM   5201  CA  LEU   288      27.294   6.861  -4.569  1.00  0.00                              
ATOM   5203  CB  LEU   288      26.162   6.831  -3.533  1.00  0.00                              
ATOM   5205  C   LEU   288      28.521   6.205  -3.992  1.00  0.00                              
ATOM   5207  O   LEU   288      28.741   5.038  -4.234  1.00  0.00                              
ATOM   5209  CG  LEU   288      26.510   7.330  -2.125  1.00  0.00                              
ATOM   5211  CD1 LEU   288      26.872   8.809  -2.170  1.00  0.00                              
ATOM   5213  CD2 LEU   288      25.337   7.096  -1.182  1.00  0.00                              
TER 
END
