
#######################################################
#                                                     #
#                        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   42 (   42),  selected   42 , name T0356TS464_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected   42 , name T0356_D3.pdb
# PARAMETERS: T0356TS464_4-D3.T0356_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:    18       354 - 371         4.94    18.18
  LONGEST_CONTINUOUS_SEGMENT:    18       355 - 372         4.84    18.70
  LCS_AVERAGE:     11.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       450 - 455         1.20    14.71
  LONGEST_CONTINUOUS_SEGMENT:     6       452 - 457         1.87    25.22
  LCS_AVERAGE:      3.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       396 - 400         0.76    16.39
  LONGEST_CONTINUOUS_SEGMENT:     5       451 - 455         0.65    16.97
  LCS_AVERAGE:      3.04

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:  120
LCS_GDT     D     353     D     353      3    3   16     0    3    3    3    3    4    4    5    8    9   13   16   19   19   20   20   22   23   23   26 
LCS_GDT     F     354     F     354      3    3   18     1    3    3    8    8    8    8    8   10   12   13   17   19   19   20   21   22   23   24   26 
LCS_GDT     Y     355     Y     355      3    3   18     0    3    4    8    8    8    8   10   11   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     L     356     L     356      3    3   18     3    4    4    8    8    8    8   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     P     357     P     357      4    4   18     3    4    4    4    4    5    8   10   11   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     P     358     P     358      4    4   18     3    4    4    4    4    5    7   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     E     359     E     359      4    4   18     3    4    4    4    5    6    8   11   13   15   16   17   19   19   20   21   22   23   24   26 
LCS_GDT     G     360     G     360      4    4   18     3    4    4    5    5    5    7   10   11   13   16   17   19   19   20   21   22   22   24   27 
LCS_GDT     C     361     C     361      3    4   18     3    3    4    5    5    6    8   11   13   15   16   17   19   19   20   21   22   22   25   27 
LCS_GDT     S     362     S     362      4    5   18     3    3    4    8    8    8    8   11   13   15   16   17   19   19   20   21   22   22   25   27 
LCS_GDT     Y     363     Y     363      4    5   18     3    3    4    8    8    8    8   11   13   15   16   17   19   19   20   21   22   22   25   26 
LCS_GDT     R     364     R     364      4    5   18     3    3    4    8    8    8    8   10   11   15   16   17   19   19   20   21   22   22   22   24 
LCS_GDT     L     365     L     365      4    5   18     3    3    4    8    8    8    8   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     A     366     A     366      4    5   18     3    3    4    8    8    8    8   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     V     367     V     367      3    3   18     3    3    3    4    4    6    7   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     V     368     V     368      3    3   18     3    3    3    4    4    5    7    8   11   12   14   15   16   18   19   21   22   23   25   27 
LCS_GDT     T     369     T     369      3    4   18     1    3    4    4    4    4    5    8    9   12   13   15   16   18   19   21   22   23   25   27 
LCS_GDT     I     370     I     370      3    4   18     3    3    4    4    4    6    6    8    8   11   13   15   16   18   19   21   22   23   24   26 
LCS_GDT     K     371     K     371      3    4   18     3    3    4    4    4    4    6    8    8    8   11   12   14   17   19   20   22   23   23   26 
LCS_GDT     K     372     K     372      3    4   18     3    3    3    4    4    4    6    8    8    9   11   13   16   18   19   20   22   23   24   26 
LCS_GDT     Q     373     Q     373      3    4   10     3    3    3    4    4    4    6    7    8    8   11   12   13   15   16   18   19   20   22   24 
LCS_GDT     Y     374     Y     374      3    4   10     3    3    3    4    4    4    6    7    8    8   11   12   13   15   16   18   22   22   23   24 
LCS_GDT     A     375     A     375      0    4   10     0    0    3    4    4    4    5    7    7    8    9   12   15   18   19   20   22   23   23   26 
LCS_GDT     K     396     K     396      5    5    5     3    5    5    5    5    5    5    5    7    8   11   12   13   13   13   15   15   16   19   21 
LCS_GDT     F     397     F     397      5    5    8     4    5    5    5    5    5    5    5    7    8   11   12   13   13   16   19   20   23   25   27 
LCS_GDT     V     398     V     398      5    5    8     4    5    5    5    5    5    5    5    7    8   11   12   13   16   19   20   22   23   25   27 
LCS_GDT     I     399     I     399      5    5    8     4    5    5    5    5    6    7   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     V     400     V     400      5    5    8     4    5    5    5    5    6    7   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     S     445     S     445      4    4    8     3    3    4    5    5    5    6    7    7    7    9    9   12   13   14   16   18   19   20   25 
LCS_GDT     G     446     G     446      4    4    8     3    3    4    4    4    4    6    6    7    8   10   11   12   13   14   20   22   23   25   27 
LCS_GDT     L     447     L     447      4    4    8     3    4    4    4    4    4    6    7    7    8   10   11   12   13   14   16   22   23   25   27 
LCS_GDT     G     448     G     448      4    4    8     0    3    4    4    4    4    6    6    7    8   10   11   12   14   19   20   22   23   25   27 
LCS_GDT     S     449     S     449      3    4   10     1    3    3    4    4    5    6    8   10   10   12   15   16   17   19   20   22   23   25   27 
LCS_GDT     K     450     K     450      3    6   10     3    3    5    6    6    6    6    8   10   10   12   15   16   17   19   20   22   23   25   27 
LCS_GDT     M     451     M     451      5    6   10     3    5    5    6    6    6    7    8   10   10   12   15   16   17   19   20   22   23   25   27 
LCS_GDT     G     452     G     452      5    6   10     4    5    5    6    6    6    7    7    8   10   12   15   16   17   18   20   22   23   25   27 
LCS_GDT     L     453     L     453      5    6   10     4    5    5    6    6    6    7    8   10   10   12   15   16   17   19   20   22   23   25   27 
LCS_GDT     D     454     D     454      5    6   10     4    5    5    6    6    6    7    8   10   10   12   15   16   17   19   20   22   23   25   27 
LCS_GDT     A     455     A     455      5    6   10     4    5    5    6    6    6    7   11   13   15   16   17   19   19   20   21   22   23   25   27 
LCS_GDT     T     456     T     456      3    6   10     3    3    3    4    5    6    7   11   13   15   16   17   19   19   20   21   21   22   23   25 
LCS_GDT     N     457     N     457      3    6   10     3    3    3    4    5    6    7    7    8    8   11   12   13   13   20   20   20   21   22   23 
LCS_GDT     W     467     W     467      0    0   10     0    2    4    4    4    5    6    7    8    9   11   15   16   17   19   20   22   23   25   27 
LCS_AVERAGE  LCS_A:   5.91  (   3.04    3.65   11.05 )

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      5      5      8      8      8      8     11     13     15     16     17     19     19     20     21     22     23     25     27 
GDT PERCENT_CA   3.33   4.17   4.17   6.67   6.67   6.67   6.67   9.17  10.83  12.50  13.33  14.17  15.83  15.83  16.67  17.50  18.33  19.17  20.83  22.50
GDT RMS_LOCAL    0.30   0.65   0.65   1.51   1.51   1.51   1.51   3.19   3.34   3.59   3.73   3.96   4.44   4.44   4.74   5.69   5.85   6.42   7.22   7.53
GDT RMS_ALL_CA  17.62  16.97  16.97  15.50  15.50  15.50  15.50  16.88  16.89  16.89  16.88  16.99  17.09  17.09  17.39  17.08  18.23  10.64  10.76  10.65

#      Molecule1      Molecule2       DISTANCE
LGA    D     353      D     353          8.355
LGA    F     354      F     354          9.819
LGA    Y     355      Y     355          7.068
LGA    L     356      L     356          3.992
LGA    P     357      P     357          4.983
LGA    P     358      P     358          4.151
LGA    E     359      E     359          2.125
LGA    G     360      G     360          5.711
LGA    C     361      C     361          2.323
LGA    S     362      S     362          3.970
LGA    Y     363      Y     363          3.997
LGA    R     364      R     364          4.554
LGA    L     365      L     365          1.859
LGA    A     366      A     366          3.761
LGA    V     367      V     367          4.026
LGA    V     368      V     368         10.572
LGA    T     369      T     369         14.585
LGA    I     370      I     370         14.796
LGA    K     371      K     371         18.074
LGA    K     372      K     372         20.915
LGA    Q     373      Q     373         25.053
LGA    Y     374      Y     374         22.132
LGA    A     375      A     375         20.925
LGA    K     396      K     396         17.200
LGA    F     397      F     397         12.979
LGA    V     398      V     398          8.815
LGA    I     399      I     399          3.104
LGA    V     400      V     400          3.003
LGA    S     445      S     445         34.132
LGA    G     446      G     446         36.818
LGA    L     447      L     447         35.254
LGA    G     448      G     448         29.401
LGA    S     449      S     449         28.859
LGA    K     450      K     450         28.555
LGA    M     451      M     451         23.428
LGA    G     452      G     452         18.538
LGA    L     453      L     453         11.750
LGA    D     454      D     454          6.916
LGA    A     455      A     455          2.200
LGA    T     456      T     456          3.900
LGA    N     457      N     457          9.433
LGA    W     467      W     467         26.340

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   42  120    4.0     11    3.19     9.375     7.901     0.335

LGA_LOCAL      RMSD =  3.187  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.892  Number of atoms =   42 
Std_ALL_ATOMS  RMSD = 10.281  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.715940 * X  +  -0.224680 * Y  +  -0.661021 * Z  +  61.703747
  Y_new =   0.488338 * X  +   0.515494 * Y  +  -0.704125 * Z  +  66.616859
  Z_new =   0.498955 * X  +  -0.826913 * Y  +  -0.259343 * Z  +  84.183846 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.874708    1.266884  [ DEG:  -107.4129     72.5871 ]
  Theta =  -0.522393   -2.619200  [ DEG:   -29.9309   -150.0691 ]
  Phi   =   2.542986   -0.598607  [ DEG:   145.7024    -34.2976 ]
 
# 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: T0356TS464_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_4-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   42  120   4.0   11   3.19   7.901    10.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_4-D3
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM    121  CA  ASP   353      52.374  69.660  68.325  1.00  0.00
ATOM    122  CA  PHE   354      50.045  70.150  71.268  1.00  0.00
ATOM    123  CA  TYR   355      49.240  66.414  71.446  1.00  0.00
ATOM    124  CA  LEU   356      52.948  65.500  71.852  1.00  0.00
ATOM    125  CA  PRO   357      53.229  68.158  74.558  1.00  0.00
ATOM    126  CA  PRO   358      50.256  67.310  76.764  1.00  0.00
ATOM    127  CA  GLU   359      50.764  63.521  76.421  1.00  0.00
ATOM    128  CA  GLY   360      54.460  63.174  75.645  1.00  0.00
ATOM    129  CA  CYS   361      53.848  61.238  72.422  1.00  0.00
ATOM    130  CA  SER   362      55.833  60.576  69.251  1.00  0.00
ATOM    131  CA  TYR   363      54.682  62.640  66.261  1.00  0.00
ATOM    132  CA  ARG   364      53.164  59.472  64.694  1.00  0.00
ATOM    133  CA  LEU   365      51.041  58.506  67.772  1.00  0.00
ATOM    134  CA  ALA   366      49.679  62.085  67.715  1.00  0.00
ATOM    135  CA  VAL   367      48.521  61.663  64.072  1.00  0.00
ATOM    136  CA  VAL   368      46.973  58.217  64.442  1.00  0.00
ATOM    137  CA  THR   369      45.070  59.332  67.573  1.00  0.00
ATOM    138  CA  ILE   370      43.818  62.003  65.161  1.00  0.00
ATOM    139  CA  LYS   371      42.595  59.504  62.608  1.00  0.00
ATOM    140  CA  LYS   372      40.561  57.665  65.233  1.00  0.00
ATOM    141  CA  GLN   373      39.290  60.626  67.258  1.00  0.00
ATOM    142  CA  TYR   374      37.771  61.680  63.703  1.00  0.00
ATOM    143  CA  ALA   375      36.573  58.107  63.197  1.00  0.00
ATOM    144  CA  LYS   396      37.211  56.866  57.310  1.00  0.00
ATOM    145  CA  PHE   397      38.877  60.268  57.811  1.00  0.00
ATOM    146  CA  VAL   398      42.434  60.061  56.427  1.00  0.00
ATOM    147  CA  ILE   399      45.686  61.473  57.828  1.00  0.00
ATOM    148  CA  VAL   400      48.461  62.777  55.601  1.00  0.00
ATOM    149  CA  SER   445      37.714  69.390  65.490  1.00  0.00
ATOM    150  CA  GLY   446      35.094  72.021  64.688  1.00  0.00
ATOM    151  CA  LEU   447      35.747  71.817  60.932  1.00  0.00
ATOM    152  CA  GLY   448      35.165  68.028  60.860  1.00  0.00
ATOM    153  CA  SER   449      31.659  68.345  62.322  1.00  0.00
ATOM    154  CA  LYS   450      30.516  71.076  59.949  1.00  0.00
ATOM    155  CA  MET   451      32.230  70.119  56.692  1.00  0.00
ATOM    156  CA  GLY   452      32.809  66.776  54.970  1.00  0.00
ATOM    157  CA  LEU   453      36.559  66.469  55.597  1.00  0.00
ATOM    158  CA  ASP   454      38.266  63.807  53.468  1.00  0.00
ATOM    159  CA  ALA   455      41.886  64.050  54.647  1.00  0.00
ATOM    160  CA  THR   456      43.784  66.169  57.195  1.00  0.00
ATOM    161  CA  ASN   457      47.338  66.987  56.132  1.00  0.00
ATOM    162  CA  TRP   467      51.318  49.745  51.605  1.00  0.00
TER
END
