
#######################################################
#                                                     #
#                        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    7 (   28),  selected    7 , name T0372TS383_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    7 , name T0372_D1.pdb
# PARAMETERS: T0372TS383_4-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:     6       290 - 297         4.51     6.41
  LCS_AVERAGE:      4.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       294 - 297         1.56     7.67
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         1.82    10.74
  LCS_AVERAGE:      2.27

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       294 - 296         0.05     6.55
  LONGEST_CONTINUOUS_SEGMENT:     3       295 - 297         0.20    10.18
  LONGEST_CONTINUOUS_SEGMENT:     3       296 - 298         0.43    14.22
  LCS_AVERAGE:      1.70

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      0    0    6     0    0    0    0    2    2    4    4    5    5    5    5    5    6    6    6    7    7    7    7 
LCS_GDT     Y     291     Y     291      0    0    6     0    0    0    1    2    2    4    4    5    5    5    5    5    6    6    6    7    7    7    7 
LCS_GDT     C     294     C     294      3    4    6     3    3    3    4    4    4    5    5    5    5    5    5    5    6    6    6    7    7    7    7 
LCS_GDT     L     295     L     295      3    4    6     3    3    3    4    4    4    5    5    5    5    5    5    5    6    6    6    7    7    7    7 
LCS_GDT     K     296     K     296      3    4    6     3    3    3    4    4    4    5    5    5    5    5    5    5    6    6    6    7    7    7    7 
LCS_GDT     D     297     D     297      3    4    6     3    3    3    4    4    4    5    5    5    5    5    5    5    6    6    6    7    7    7    7 
LCS_GDT     H     298     H     298      3    4    5     3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    7    7    7    7 
LCS_AVERAGE  LCS_A:   2.87  (   1.70    2.27    4.65 )

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      3      4      4      4      5      5      5      5      5      5      5      6      6      6      7      7      7      7 
GDT PERCENT_CA   2.38   2.38   2.38   3.17   3.17   3.17   3.97   3.97   3.97   3.97   3.97   3.97   3.97   4.76   4.76   4.76   5.56   5.56   5.56   5.56
GDT RMS_LOCAL    0.05   0.05   0.05   1.56   1.56   1.56   2.46   2.46   2.46   2.46   2.46   2.46   2.46   4.51   4.51   4.51   5.89   5.89   5.89   5.89
GDT RMS_ALL_CA   6.55   6.55   6.55   7.67   7.67   7.67   9.34   9.34   9.34   9.34   9.34   9.34   9.34   6.41   6.41   6.41   5.89   5.89   5.89   5.89

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         19.249
LGA    Y     291      Y     291         14.475
LGA    C     294      C     294          2.857
LGA    L     295      L     295          2.880
LGA    K     296      K     296          0.933
LGA    D     297      D     297          3.075
LGA    H     298      H     298          1.843

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7  126    4.0      5    2.46     3.571     3.237     0.196

LGA_LOCAL      RMSD =  2.457  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.337  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  5.890  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.112148 * X  +   0.882345 * Y  +  -0.457044 * Z  +   7.351963
  Y_new =  -0.979391 * X  +   0.020398 * Y  +  -0.200941 * Z  +  52.026211
  Z_new =  -0.167977 * X  +   0.470160 * Y  +   0.866449 * Z  + -64.512375 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.497166   -2.644426  [ DEG:    28.4855   -151.5145 ]
  Theta =   0.168777    2.972815  [ DEG:     9.6702    170.3298 ]
  Phi   =  -1.456785    1.684808  [ DEG:   -83.4676     96.5324 ]
 
# 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_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS383_4-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7  126   4.0    5   2.46   3.237     5.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS383_4-D1
PFRMAT TS
TARGET T0372
MODEL 4
PARENT 1cjwA
ATOM    505  N   LYS   290      35.600  46.374 -11.232  1.00  0.00
ATOM    506  CA  LYS   290      34.784  46.829 -10.106  1.00  0.00
ATOM    507  C   LYS   290      33.305  46.966 -10.461  1.00  0.00
ATOM    508  O   LYS   290      32.940  47.579 -11.469  1.00  0.00
ATOM    509  N   TYR   291      32.458  46.411  -9.605  1.00  0.00
ATOM    510  CA  TYR   291      31.020  46.464  -9.805  1.00  0.00
ATOM    511  C   TYR   291      30.374  47.163  -8.613  1.00  0.00
ATOM    512  O   TYR   291      30.785  46.955  -7.468  1.00  0.00
ATOM    513  N   CYS   294      29.422  48.048  -8.894  1.00  0.00
ATOM    514  CA  CYS   294      28.694  48.791  -7.861  1.00  0.00
ATOM    515  C   CYS   294      27.221  48.736  -8.246  1.00  0.00
ATOM    516  O   CYS   294      26.799  49.419  -9.183  1.00  0.00
ATOM    517  N   LEU   295      26.439  47.924  -7.539  1.00  0.00
ATOM    518  CA  LEU   295      25.030  47.806  -7.857  1.00  0.00
ATOM    519  C   LEU   295      24.881  47.291  -9.274  1.00  0.00
ATOM    520  O   LEU   295      25.525  46.310  -9.642  1.00  0.00
ATOM    521  N   LYS   296      24.066  47.964 -10.080  1.00  0.00
ATOM    522  CA  LYS   296      23.861  47.568 -11.471  1.00  0.00
ATOM    523  C   LYS   296      24.681  48.433 -12.435  1.00  0.00
ATOM    524  O   LYS   296      24.533  48.331 -13.659  1.00  0.00
ATOM    525  N   ASP   297      25.555  49.269 -11.879  1.00  0.00
ATOM    526  CA  ASP   297      26.406  50.157 -12.670  1.00  0.00
ATOM    527  C   ASP   297      27.646  49.456 -13.216  1.00  0.00
ATOM    528  O   ASP   297      28.248  48.625 -12.535  1.00  0.00
ATOM    529  N   HIS   298      28.014  49.783 -14.450  1.00  0.00
ATOM    530  CA  HIS   298      29.210  49.225 -15.084  1.00  0.00
ATOM    531  C   HIS   298      30.080  50.423 -15.478  1.00  0.00
ATOM    532  O   HIS   298      29.563  51.476 -15.876  1.00  0.00
TER
END
