
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0298TS550_1_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   18 , name T0298_D1.pdb
# PARAMETERS: T0298TS550_1_2-D1.T0298_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:    18       316 - 333         2.15     2.15
  LCS_AVERAGE:     12.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       317 - 333         1.44     2.29
  LCS_AVERAGE:     11.04

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       318 - 333         0.89     2.49
  LCS_AVERAGE:      9.91

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:  148
LCS_GDT     V     316     V     316      4    5   18     0    4    4    4    4    5    5    6   12   14   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     R     317     R     317      4   17   18     3    4    4    4    5   10   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     318     K     318     16   17   18     3    4    5   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     G     319     G     319     16   17   18     3    4   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     320     A     320     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     321     A     321     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     322     L     322     16   17   18     6   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     N     323     N     323     16   17   18     6   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     324     A     324     16   17   18    10   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     V     325     V     325     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     326     L     326     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     327     L     327     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     G     328     G     328     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     E     329     E     329     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     330     L     330     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     331     L     331     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     I     332     I     332     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     333     K     333     16   17   18    11   14   15   16   16   16   17   17   17   17   18   18   18   18   18   18   18   18   18   18 
LCS_AVERAGE  LCS_A:  11.04  (   9.91   11.04   12.16 )

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     11     14     15     16     16     16     17     17     17     17     18     18     18     18     18     18     18     18     18     18 
GDT PERCENT_CA   7.43   9.46  10.14  10.81  10.81  10.81  11.49  11.49  11.49  11.49  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16
GDT RMS_LOCAL    0.34   0.48   0.63   0.89   0.89   0.89   1.44   1.44   1.44   1.44   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15
GDT RMS_ALL_CA   2.36   2.35   2.38   2.49   2.49   2.49   2.29   2.29   2.29   2.29   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          7.277
LGA    R     317      R     317          3.902
LGA    K     318      K     318          2.919
LGA    G     319      G     319          2.019
LGA    A     320      A     320          0.861
LGA    A     321      A     321          0.514
LGA    L     322      L     322          0.946
LGA    N     323      N     323          1.031
LGA    A     324      A     324          0.679
LGA    V     325      V     325          0.662
LGA    L     326      L     326          0.460
LGA    L     327      L     327          0.489
LGA    G     328      G     328          1.161
LGA    E     329      E     329          1.011
LGA    L     330      L     330          1.083
LGA    L     331      L     331          1.545
LGA    I     332      I     332          1.612
LGA    K     333      K     333          1.208

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  148    4.0     17    1.44    10.980    11.113     1.107

LGA_LOCAL      RMSD =  1.436  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.298  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  2.153  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.397633 * X  +  -0.275056 * Y  +  -0.875347 * Z  + 112.362335
  Y_new =   0.366201 * X  +  -0.922309 * Y  +   0.123463 * Z  +  63.704693
  Z_new =  -0.841300 * X  +  -0.271460 * Y  +   0.467466 * Z  +  74.714546 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.526111    2.615481  [ DEG:   -30.1440    149.8560 ]
  Theta =   0.999683    2.141910  [ DEG:    57.2776    122.7224 ]
  Phi   =   2.397322   -0.744271  [ DEG:   137.3564    -42.6436 ]
 
# 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: T0298TS550_1_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS550_1_2-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  148   4.0   17   1.44  11.113     2.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS550_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1f2k_B
ATOM    545  N   VAL   316     -12.562  66.783  10.506  1.00  0.00
ATOM    546  CA  VAL   316     -13.963  66.815  10.111  1.00  0.00
ATOM    547  C   VAL   316     -14.080  66.215   8.710  1.00  0.00
ATOM    548  O   VAL   316     -13.089  66.135   7.998  1.00  0.00
ATOM    549  N   ARG   317     -15.258  65.723   8.390  1.00  0.00
ATOM    550  CA  ARG   317     -15.514  65.131   7.089  1.00  0.00
ATOM    551  C   ARG   317     -16.267  66.157   6.224  1.00  0.00
ATOM    552  O   ARG   317     -17.318  66.678   6.607  1.00  0.00
ATOM    553  N   LYS   318     -15.628  66.203   4.023  1.00  0.00
ATOM    554  CA  LYS   318     -17.054  66.413   4.240  1.00  0.00
ATOM    555  C   LYS   318     -17.498  67.838   3.999  1.00  0.00
ATOM    556  O   LYS   318     -18.539  68.089   3.392  1.00  0.00
ATOM    557  N   GLY   319     -16.696  68.783   4.448  1.00  0.00
ATOM    558  CA  GLY   319     -17.091  70.172   4.301  1.00  0.00
ATOM    559  C   GLY   319     -17.121  70.635   2.870  1.00  0.00
ATOM    560  O   GLY   319     -17.919  71.505   2.529  1.00  0.00
ATOM    561  N   ALA   320     -16.267  70.052   2.030  1.00  0.00
ATOM    562  CA  ALA   320     -16.204  70.445   0.628  1.00  0.00
ATOM    563  C   ALA   320     -17.506  70.014  -0.030  1.00  0.00
ATOM    564  O   ALA   320     -18.140  70.777  -0.802  1.00  0.00
ATOM    565  N   ALA   321     -17.903  68.784   0.287  1.00  0.00
ATOM    566  CA  ALA   321     -19.143  68.244  -0.237  1.00  0.00
ATOM    567  C   ALA   321     -20.322  69.188   0.115  1.00  0.00
ATOM    568  O   ALA   321     -21.036  69.624  -0.774  1.00  0.00
ATOM    569  N   LEU   322     -20.486  69.530   1.389  1.00  0.00
ATOM    570  CA  LEU   322     -21.565  70.404   1.836  1.00  0.00
ATOM    571  C   LEU   322     -21.565  71.733   1.087  1.00  0.00
ATOM    572  O   LEU   322     -22.597  72.217   0.676  1.00  0.00
ATOM    573  N   ASN   323     -20.399  72.329   0.923  1.00  0.00
ATOM    574  CA  ASN   323     -20.296  73.599   0.228  1.00  0.00
ATOM    575  C   ASN   323     -20.813  73.439  -1.202  1.00  0.00
ATOM    576  O   ASN   323     -21.566  74.285  -1.695  1.00  0.00
ATOM    577  N   ALA   324     -20.436  72.362  -1.876  1.00  0.00
ATOM    578  CA  ALA   324     -20.906  72.213  -3.241  1.00  0.00
ATOM    579  C   ALA   324     -22.416  72.121  -3.310  1.00  0.00
ATOM    580  O   ALA   324     -23.043  72.963  -3.936  1.00  0.00
ATOM    581  N   VAL   325     -22.989  71.131  -2.626  1.00  0.00
ATOM    582  CA  VAL   325     -24.438  70.946  -2.573  1.00  0.00
ATOM    583  C   VAL   325     -25.198  72.172  -2.044  1.00  0.00
ATOM    584  O   VAL   325     -26.209  72.570  -2.610  1.00  0.00
ATOM    585  N   LEU   326     -24.731  72.759  -0.951  1.00  0.00
ATOM    586  CA  LEU   326     -25.408  73.918  -0.395  1.00  0.00
ATOM    587  C   LEU   326     -25.355  75.101  -1.348  1.00  0.00
ATOM    588  O   LEU   326     -26.246  75.932  -1.346  1.00  0.00
ATOM    589  N   LEU   327     -24.318  75.166  -2.174  1.00  0.00
ATOM    590  CA  LEU   327     -24.170  76.272  -3.122  1.00  0.00
ATOM    591  C   LEU   327     -25.235  76.150  -4.164  1.00  0.00
ATOM    592  O   LEU   327     -25.945  77.112  -4.484  1.00  0.00
ATOM    593  N   GLY   328     -25.309  74.955  -4.726  1.00  0.00
ATOM    594  CA  GLY   328     -26.279  74.668  -5.755  1.00  0.00
ATOM    595  C   GLY   328     -27.658  74.989  -5.182  1.00  0.00
ATOM    596  O   GLY   328     -28.403  75.751  -5.768  1.00  0.00
ATOM    597  N   GLU   329     -27.984  74.458  -4.006  1.00  0.00
ATOM    598  CA  GLU   329     -29.284  74.774  -3.404  1.00  0.00
ATOM    599  C   GLU   329     -29.508  76.283  -3.359  1.00  0.00
ATOM    600  O   GLU   329     -30.517  76.788  -3.868  1.00  0.00
ATOM    601  N   LEU   330     -28.561  77.020  -2.782  1.00  0.00
ATOM    602  CA  LEU   330     -28.732  78.467  -2.713  1.00  0.00
ATOM    603  C   LEU   330     -29.006  79.025  -4.114  1.00  0.00
ATOM    604  O   LEU   330     -29.770  79.970  -4.280  1.00  0.00
ATOM    605  N   LEU   331     -28.360  78.461  -5.119  1.00  0.00
ATOM    606  CA  LEU   331     -28.560  78.977  -6.463  1.00  0.00
ATOM    607  C   LEU   331     -30.022  78.709  -6.900  1.00  0.00
ATOM    608  O   LEU   331     -30.791  79.615  -7.311  1.00  0.00
ATOM    609  N   ILE   332     -30.410  77.447  -6.774  1.00  0.00
ATOM    610  CA  ILE   332     -31.737  77.076  -7.168  1.00  0.00
ATOM    611  C   ILE   332     -32.787  77.889  -6.436  1.00  0.00
ATOM    612  O   ILE   332     -33.617  78.513  -7.096  1.00  0.00
ATOM    613  N   LYS   333     -32.756  77.914  -5.102  1.00  0.00
ATOM    614  CA  LYS   333     -33.760  78.686  -4.371  1.00  0.00
ATOM    615  C   LYS   333     -33.833  80.136  -4.946  1.00  0.00
ATOM    616  O   LYS   333     -34.903  80.752  -4.999  1.00  0.00
TER
END
