
#######################################################
#                                                     #
#                        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    8 (   32),  selected    8 , name T0372TS383_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    8 , name T0372_D1.pdb
# PARAMETERS: T0372TS383_5-D1.T0372_D1.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:     8       290 - 298         4.31     4.31
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 296         1.66     5.22
  LONGEST_CONTINUOUS_SEGMENT:     5       294 - 298         1.87     8.34
  LCS_AVERAGE:      3.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.35    11.58
  LCS_AVERAGE:      2.78

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:  126
LCS_GDT     K     290     K     290      3    3    8     0    3    3    3    3    3    4    5    5    6    6    7    7    7    8    8    8    8    8    8 
LCS_GDT     Y     291     Y     291      3    5    8     1    3    3    4    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     M     292     M     292      3    5    8     0    3    3    4    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     C     294     C     294      3    5    8     3    3    3    4    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     L     295     L     295      4    5    8     4    4    4    4    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     K     296     K     296      4    5    8     4    4    4    4    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     D     297     D     297      4    5    8     4    4    4    4    4    5    6    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     H     298     H     298      4    5    8     4    4    4    4    4    5    5    6    6    6    7    7    7    7    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   4.30  (   2.78    3.77    6.35 )

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      4      4      4      4      5      5      6      6      6      6      7      7      7      7      8      8      8      8      8      8 
GDT PERCENT_CA   3.17   3.17   3.17   3.17   3.97   3.97   4.76   4.76   4.76   4.76   5.56   5.56   5.56   5.56   6.35   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.35   0.35   0.35   0.35   1.66   1.66   2.58   2.58   2.58   2.58   3.31   3.31   3.31   3.31   4.31   4.31   4.31   4.31   4.31   4.31
GDT RMS_ALL_CA  11.58  11.58  11.58  11.58   5.22   5.22   4.88   4.88   4.88   4.88   4.68   4.68   4.68   4.68   4.31   4.31   4.31   4.31   4.31   4.31

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          8.885
LGA    Y     291      Y     291          2.821
LGA    M     292      M     292          2.657
LGA    C     294      C     294          1.801
LGA    L     295      L     295          1.056
LGA    K     296      K     296          2.935
LGA    D     297      D     297          3.478
LGA    H     298      H     298          8.461

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  126    4.0      6    2.58     4.365     4.267     0.223

LGA_LOCAL      RMSD =  2.585  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.881  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.313  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.411175 * X  +  -0.910740 * Y  +   0.038572 * Z  +  97.075577
  Y_new =   0.081406 * X  +  -0.078832 * Y  +  -0.993559 * Z  +  83.484177
  Z_new =   0.907914 * X  +  -0.405386 * Y  +   0.106553 * Z  +  11.310776 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.313767    1.827826  [ DEG:   -75.2733    104.7267 ]
  Theta =  -1.138281   -2.003311  [ DEG:   -65.2187   -114.7813 ]
  Phi   =   2.946137   -0.195455  [ DEG:   168.8012    -11.1988 ]
 
# 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: T0372TS383_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS383_5-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  126   4.0    6   2.58   4.267     4.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS383_5-D1
PFRMAT TS
TARGET T0372
MODEL 5
PARENT 1yvoA
ATOM    529  N   LYS   290      30.071  42.947   0.282  1.00  0.00
ATOM    530  CA  LYS   290      28.843  42.899  -0.526  1.00  0.00
ATOM    531  C   LYS   290      27.625  43.579   0.130  1.00  0.00
ATOM    532  O   LYS   290      26.477  43.145  -0.056  1.00  0.00
ATOM    533  N   TYR   291      27.880  44.633   0.904  1.00  0.00
ATOM    534  CA  TYR   291      26.804  45.350   1.588  1.00  0.00
ATOM    535  C   TYR   291      26.110  46.337   0.670  1.00  0.00
ATOM    536  O   TYR   291      25.026  46.838   0.990  1.00  0.00
ATOM    537  N   MET   292      26.726  46.613  -0.479  1.00  0.00
ATOM    538  CA  MET   292      26.127  47.569  -1.401  1.00  0.00
ATOM    539  C   MET   292      26.220  47.095  -2.828  1.00  0.00
ATOM    540  O   MET   292      26.803  46.046  -3.111  1.00  0.00
ATOM    541  N   CYS   294      25.628  47.862  -3.729  1.00  0.00
ATOM    542  CA  CYS   294      25.697  47.541  -5.147  1.00  0.00
ATOM    543  C   CYS   294      25.781  48.824  -5.966  1.00  0.00
ATOM    544  O   CYS   294      25.215  49.853  -5.586  1.00  0.00
ATOM    545  N   LEU   295      26.505  48.761  -7.081  1.00  0.00
ATOM    546  CA  LEU   295      26.470  49.819  -8.084  1.00  0.00
ATOM    547  C   LEU   295      27.001  49.232  -9.369  1.00  0.00
ATOM    548  O   LEU   295      27.809  48.302  -9.331  1.00  0.00
ATOM    549  N   LYS   296      26.557  49.783 -10.501  1.00  0.00
ATOM    550  CA  LYS   296      27.001  49.319 -11.825  1.00  0.00
ATOM    551  C   LYS   296      26.710  47.831 -12.045  1.00  0.00
ATOM    552  O   LYS   296      27.412  47.158 -12.796  1.00  0.00
ATOM    553  N   ASP   297      25.659  47.320 -11.410  1.00  0.00
ATOM    554  CA  ASP   297      25.308  45.903 -11.511  1.00  0.00
ATOM    555  C   ASP   297      26.228  44.889 -10.827  1.00  0.00
ATOM    556  O   ASP   297      26.205  43.701 -11.165  1.00  0.00
ATOM    557  N   HIS   298      27.045  45.338  -9.875  1.00  0.00
ATOM    558  CA  HIS   298      27.892  44.414  -9.096  1.00  0.00
ATOM    559  C   HIS   298      27.862  44.707  -7.596  1.00  0.00
ATOM    560  O   HIS   298      27.653  45.849  -7.209  1.00  0.00
TER
END
