
#######################################################
#                                                     #
#                        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 T0356TS383_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected   18 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_2-D1.T0356_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:    15       323 - 337         4.63    11.42
  LONGEST_CONTINUOUS_SEGMENT:    15       324 - 338         4.78    11.97
  LCS_AVERAGE:     11.34

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       329 - 335         1.57    11.37
  LCS_AVERAGE:      4.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       330 - 335         0.17    10.64
  LCS_AVERAGE:      3.41

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:  124
LCS_GDT     D     314     D     314      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0   11   11   11   12   12   12   12 
LCS_GDT     G     323     G     323      4    4   15     3    4    4    4    4    4    4    4    4    6    6    6    6   14   14   15   15   15   15   15 
LCS_GDT     R     324     R     324      4    6   15     3    4    4    4    6    6    8   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     P     325     P     325      4    6   15     3    4    5    7    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     P     326     P     326      4    6   15     4    4    5    7    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     D     327     D     327      4    6   15     4    4    5    7    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     E     328     E     328      4    6   15     4    4    5    7    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     P     329     P     329      4    7   15     4    4    5    7    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     A     330     A     330      6    7   15     6    6    6    6    6    7    7    9   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     V     331     V     331      6    7   15     6    6    6    6    6    7    7    9   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     L     332     L     332      6    7   15     6    6    6    6    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     G     333     G     333      6    7   15     6    6    6    6    6    7    7    9   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     V     334     V     334      6    7   15     6    6    6    6    6    7    7    9   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     A     335     A     335      6    7   15     6    6    6    6    7    9    9   10   10   12   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     L     336     L     336      3    4   15     3    3    5    7    7    9    9   10   10   11   12   14   14   14   14   15   15   15   15   15 
LCS_GDT     N     337     N     337      3    4   15     0    3    3    7    7    9    9   10   10   11   11   14   14   14   14   15   15   15   15   15 
LCS_GDT     E     338     E     338      3    3   15     1    3    3    3    4    4    5    7    8    8   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     V     339     V     339      3    3   13     0    3    3    3    4    4    5    7    8   10   11   11   12   12   12   12   13   13   15   15 
LCS_AVERAGE  LCS_A:   6.36  (   3.41    4.35   11.34 )

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      6      6      6      7      7      9      9     10     10     12     12     14     14     14     14     15     15     15     15     15 
GDT PERCENT_CA   4.84   4.84   4.84   5.65   5.65   7.26   7.26   8.06   8.06   9.68   9.68  11.29  11.29  11.29  11.29  12.10  12.10  12.10  12.10  12.10
GDT RMS_LOCAL    0.17   0.17   0.17   1.46   1.46   2.05   2.05   2.53   2.53   3.78   3.67   4.05   4.05   4.05   4.05   4.63   4.63   4.63   4.63   4.63
GDT RMS_ALL_CA  10.64  10.64  10.64  11.92  11.92  11.89  11.89  11.59  11.59  11.99  11.85  11.92  11.92  11.92  11.92  11.42  11.42  11.42  11.42  11.42

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         41.644
LGA    G     323      G     323         10.731
LGA    R     324      R     324          3.841
LGA    P     325      P     325          1.991
LGA    P     326      P     326          1.717
LGA    D     327      D     327          1.736
LGA    E     328      E     328          1.509
LGA    P     329      P     329          2.723
LGA    A     330      A     330          7.283
LGA    V     331      V     331          5.569
LGA    L     332      L     332          2.739
LGA    G     333      G     333          7.381
LGA    V     334      V     334          7.831
LGA    A     335      A     335          2.594
LGA    L     336      L     336          1.892
LGA    N     337      N     337          3.784
LGA    E     338      E     338          9.886
LGA    V     339      V     339         13.855

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  124    4.0     10    2.53     7.661     6.894     0.381

LGA_LOCAL      RMSD =  2.527  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.560  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  8.627  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.299496 * X  +   0.069211 * Y  +  -0.951584 * Z  + 119.862473
  Y_new =   0.282577 * X  +  -0.959053 * Y  +   0.019183 * Z  +  58.975849
  Z_new =  -0.911292 * X  +  -0.274641 * Y  +  -0.306789 * Z  + 133.138443 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.411431    0.730162  [ DEG:  -138.1648     41.8352 ]
  Theta =   1.146410    1.995182  [ DEG:    65.6845    114.3155 ]
  Phi   =   0.756340   -2.385253  [ DEG:    43.3351   -136.6649 ]
 
# 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: T0356TS383_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_2-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  124   4.0   10   2.53   6.894     8.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_2-D1
PFRMAT TS
TARGET t0356
MODEL 2
PARENT 1i0rA
ATOM    537  N   ASP   314      43.145  58.225  79.698  1.00  0.00
ATOM    538  CA  ASP   314      44.047  57.125  79.437  1.00  0.00
ATOM    539  C   ASP   314      45.387  57.618  78.851  1.00  0.00
ATOM    540  O   ASP   314      46.276  56.820  78.518  1.00  0.00
ATOM    541  N   GLY   323      45.541  58.935  78.753  1.00  0.00
ATOM    542  CA  GLY   323      46.723  59.555  78.169  1.00  0.00
ATOM    543  C   GLY   323      48.020  59.392  78.941  1.00  0.00
ATOM    544  O   GLY   323      48.012  59.107  80.139  1.00  0.00
ATOM    545  N   ARG   324      49.131  59.581  78.233  1.00  0.00
ATOM    546  CA  ARG   324      50.453  59.525  78.840  1.00  0.00
ATOM    547  C   ARG   324      50.607  60.818  79.634  1.00  0.00
ATOM    548  O   ARG   324      49.962  61.845  79.329  1.00  0.00
ATOM    549  N   PRO   325      51.434  60.763  80.670  1.00  0.00
ATOM    550  CA  PRO   325      51.679  61.948  81.475  1.00  0.00
ATOM    551  C   PRO   325      52.842  62.731  80.895  1.00  0.00
ATOM    552  O   PRO   325      53.650  62.205  80.126  1.00  0.00
ATOM    553  N   PRO   326      52.912  64.002  81.253  1.00  0.00
ATOM    554  CA  PRO   326      53.988  64.876  80.802  1.00  0.00
ATOM    555  C   PRO   326      55.059  64.869  81.861  1.00  0.00
ATOM    556  O   PRO   326      54.773  65.152  83.023  1.00  0.00
ATOM    557  N   ASP   327      56.294  64.552  81.500  1.00  0.00
ATOM    558  CA  ASP   327      57.350  64.604  82.506  1.00  0.00
ATOM    559  C   ASP   327      58.065  65.946  82.412  1.00  0.00
ATOM    560  O   ASP   327      57.935  66.679  81.422  1.00  0.00
ATOM    561  N   GLU   328      58.812  66.297  83.448  1.00  0.00
ATOM    562  CA  GLU   328      59.544  67.557  83.444  1.00  0.00
ATOM    563  C   GLU   328      60.599  67.509  82.324  1.00  0.00
ATOM    564  O   GLU   328      60.841  68.501  81.636  1.00  0.00
ATOM    565  N   PRO   329      61.225  66.349  82.146  1.00  0.00
ATOM    566  CA  PRO   329      62.218  66.177  81.085  1.00  0.00
ATOM    567  C   PRO   329      61.539  66.427  79.726  1.00  0.00
ATOM    568  O   PRO   329      62.146  67.052  78.843  1.00  0.00
ATOM    569  N   ALA   330      61.167  70.004  79.023  1.00  0.00
ATOM    570  CA  ALA   330      62.392  70.655  78.602  1.00  0.00
ATOM    571  C   ALA   330      62.681  70.441  77.125  1.00  0.00
ATOM    572  O   ALA   330      63.278  71.313  76.479  1.00  0.00
ATOM    573  N   VAL   331      62.231  69.311  76.585  1.00  0.00
ATOM    574  CA  VAL   331      62.414  69.054  75.169  1.00  0.00
ATOM    575  C   VAL   331      61.460  70.016  74.464  1.00  0.00
ATOM    576  O   VAL   331      61.787  70.567  73.410  1.00  0.00
ATOM    577  N   LEU   332      60.291  70.247  75.062  1.00  0.00
ATOM    578  CA  LEU   332      59.329  71.171  74.469  1.00  0.00
ATOM    579  C   LEU   332      59.909  72.579  74.437  1.00  0.00
ATOM    580  O   LEU   332      59.743  73.298  73.449  1.00  0.00
ATOM    581  N   GLY   333      60.577  72.984  75.514  1.00  0.00
ATOM    582  CA  GLY   333      61.184  74.313  75.559  1.00  0.00
ATOM    583  C   GLY   333      62.140  74.486  74.382  1.00  0.00
ATOM    584  O   GLY   333      62.212  75.557  73.781  1.00  0.00
ATOM    585  N   VAL   334      62.875  73.424  74.067  1.00  0.00
ATOM    586  CA  VAL   334      63.837  73.448  72.970  1.00  0.00
ATOM    587  C   VAL   334      63.172  73.345  71.597  1.00  0.00
ATOM    588  O   VAL   334      63.856  73.240  70.579  1.00  0.00
ATOM    589  N   ALA   335      61.842  73.363  71.568  1.00  0.00
ATOM    590  CA  ALA   335      61.139  73.313  70.297  1.00  0.00
ATOM    591  C   ALA   335      60.528  72.005  69.834  1.00  0.00
ATOM    592  O   ALA   335      59.743  71.999  68.884  1.00  0.00
ATOM    593  N   LEU   336      60.878  70.896  70.477  1.00  0.00
ATOM    594  CA  LEU   336      60.328  69.603  70.087  1.00  0.00
ATOM    595  C   LEU   336      58.828  69.572  70.394  1.00  0.00
ATOM    596  O   LEU   336      58.311  70.411  71.131  1.00  0.00
ATOM    597  N   ASN   337      58.128  68.606  69.817  1.00  0.00
ATOM    598  CA  ASN   337      56.698  68.470  70.058  1.00  0.00
ATOM    599  C   ASN   337      56.348  66.980  70.058  1.00  0.00
ATOM    600  O   ASN   337      56.794  66.228  69.193  1.00  0.00
ATOM    601  N   GLU   338      55.562  66.533  71.048  1.00  0.00
ATOM    602  CA  GLU   338      55.160  65.125  71.160  1.00  0.00
ATOM    603  C   GLU   338      54.361  64.659  69.948  1.00  0.00
ATOM    604  O   GLU   338      53.613  65.435  69.359  1.00  0.00
ATOM    605  N   VAL   339      54.526  63.396  69.571  1.00  0.00
ATOM    606  CA  VAL   339      53.774  62.859  68.448  1.00  0.00
ATOM    607  C   VAL   339      53.078  61.562  68.825  1.00  0.00
ATOM    608  O   VAL   339      53.709  60.628  69.321  1.00  0.00
TER
END
