
#######################################################
#                                                     #
#                        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   41 (   41),  selected   41 , name T0301TS464_3_1-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   41 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_3_1-D2.T0301_D2.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:    21       209 - 282         4.89    10.15
  LCS_AVERAGE:      8.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       299 - 328         1.98    15.82
  LCS_AVERAGE:      3.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       217 - 222         0.99    16.54
  LONGEST_CONTINUOUS_SEGMENT:     6       276 - 281         0.98    17.69
  LONGEST_CONTINUOUS_SEGMENT:     6       277 - 282         0.98    19.25
  LONGEST_CONTINUOUS_SEGMENT:     6       299 - 304         0.33    15.45
  LCS_AVERAGE:      2.30

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:  191
LCS_GDT     G     207     G     207      3    3   10     3    3    3    3    3    3    5    5    9   14   14   19   20   24   27   29   30   31   32   32 
LCS_GDT     T     208     T     208      3    3   13     3    3    3    3    4    4    6    8   10   14   16   19   22   24   27   29   30   31   32   32 
LCS_GDT     F     209     F     209      3    3   21     3    3    3    3    4    4    6    8   10   14   16   19   21   24   27   29   30   31   32   32 
LCS_GDT     K     210     K     210      3    3   21     3    3    3    3    4    4    6    8   11   14   18   20   23   25   27   29   30   31   32   32 
LCS_GDT     A     211     A     211      3    3   21     3    3    3    7    8    9   11   12   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     T     212     T     212      3    3   21     3    3    3    7    8    9   11   13   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     M     213     M     213      3    3   21     3    4    4    7    8    9   11   13   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     I     214     I     214      3    4   21     3    4    5    7   11   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     N     215     N     215      3    4   21     3    3    5    5    5    6   11   15   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     A     216     A     216      3    6   21     3    4    5    9   11   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     G     217     G     217      6    7   21     3    4    6    7   12   14   15   16   16   17   18   21   23   25   27   29   30   31   32   32 
LCS_GDT     I     218     I     218      6    7   21     3    5    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     P     219     P     219      6    7   21     3    5    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     T     220     T     220      6    7   21     3    5    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     V     221     V     221      6    7   21     3    5    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     F     222     F     222      6    7   21     3    5    6    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     P     276     P     276      6    7   21     4    4    6    7    8   14   15   16   16   17   18   24   24   25   26   26   29   31   32   32 
LCS_GDT     K     277     K     277      6    7   21     4    4    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     I     278     I     278      6    7   21     4    5    6    7   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     A     279     A     279      6    7   21     4    5    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     F     280     F     280      6    7   21     3    5    6    7    8   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     V     281     V     281      6    7   21     3    5    7    9   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     A     282     A     282      6    7   21     2    5    6    7   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     D     299     D     299      6    8   13     6    7    7    7    7    7    7    9   10   11   13   14   16   16   18   21   25   27   29   30 
LCS_GDT     I     300     I     300      6    8   13     6    7    7    7    7    7    7    9   10   11   15   16   16   20   23   25   27   28   30   31 
LCS_GDT     D     301     D     301      6    8   13     6    7    7    7    7    7    7    9   12   12   15   16   21   24   27   28   30   31   31   32 
LCS_GDT     L     302     L     302      6    8   13     6    7    7    7    7    7    7   10   12   14   17   20   22   24   27   29   30   31   32   32 
LCS_GDT     L     303     L     303      6    8   13     6    7    7    7    7    7    8   12   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     V     304     V     304      6    8   13     6    7    7    8   12   14   15   16   16   20   21   24   24   25   27   29   30   31   32   32 
LCS_GDT     A     327     A     327      3    8   13     3    4    4    5    5    6    7    8   11   12   17   20   22   24   27   29   30   31   32   32 
LCS_GDT     A     328     A     328      3    8   13     3    7    7    7    7    7    8   11   12   14   18   20   22   24   27   29   30   31   32   32 
LCS_GDT     A     329     A     329      3    4   13     3    3    3    5    5    6    7    9   12   13   17   20   22   24   27   29   30   31   32   32 
LCS_GDT     I     330     I     330      3    4   13     3    3    3    5    5    6    7    7   11   13   16   19   21   24   27   28   30   31   31   32 
LCS_GDT     P     331     P     331      3    4   11     0    3    3    5    5    6    7    8   10   10   15   15   17   22   22   23   23   23   23   28 
LCS_GDT     L     356     L     356      3    4   10     3    3    5    5    5    6    7   14   16   20   21   24   24   25   26   29   29   31   32   32 
LCS_GDT     R     357     R     357      3    6   10     3    3    5    5    5    6    7    7   10   18   21   24   24   25   26   27   29   31   32   32 
LCS_GDT     V     358     V     358      3    6   10     3    3    5    5    5    6    7   13   15   18   21   24   24   25   26   27   29   30   32   32 
LCS_GDT     G     359     G     359      3    6   10     3    3    4    5    5    6   10   10   14   18   20   24   24   25   26   26   29   30   30   32 
LCS_GDT     A     360     A     360      3    6   10     3    3    4    5    5    6    7    7    8    9   16   19   21   22   24   25   26   29   29   31 
LCS_GDT     M     376     M     376      3    6   10     1    3    3    5    5    6    7    7    8   10   11   12   13   14   19   21   22   24   27   27 
LCS_GDT     S     377     S     377      3    6    7     0    3    4    5    5    5    7    7    7    8    8    8    9   12   12   13   14   20   21   22 
LCS_AVERAGE  LCS_A:   4.66  (   2.30    3.09    8.58 )

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      7      7      9     12     14     15     16     16     20     21     24     24     25     27     29     30     31     32     32 
GDT PERCENT_CA   3.14   3.66   3.66   4.71   6.28   7.33   7.85   8.38   8.38  10.47  10.99  12.57  12.57  13.09  14.14  15.18  15.71  16.23  16.75  16.75
GDT RMS_LOCAL    0.33   0.47   0.47   1.52   1.96   2.20   2.32   2.47   2.47   3.80   3.92   4.27   4.27   4.47   5.40   8.11   5.82   5.91   6.09   6.09
GDT RMS_ALL_CA  15.45  15.53  15.53  11.69  13.40  13.73  12.34  12.63  12.63   9.89  10.00  10.00  10.00   9.90   9.49   9.49   9.80   9.41   9.36   9.36

#      Molecule1      Molecule2       DISTANCE
LGA    G     207      G     207         20.781
LGA    T     208      T     208         21.762
LGA    F     209      F     209         17.778
LGA    K     210      K     210         12.021
LGA    A     211      A     211         11.353
LGA    T     212      T     212         10.570
LGA    M     213      M     213          8.941
LGA    I     214      I     214          3.639
LGA    N     215      N     215          6.368
LGA    A     216      A     216          2.715
LGA    G     217      G     217          3.363
LGA    I     218      I     218          2.240
LGA    P     219      P     219          2.535
LGA    T     220      T     220          2.554
LGA    V     221      V     221          2.413
LGA    F     222      F     222          2.816
LGA    P     276      P     276          3.437
LGA    K     277      K     277          1.242
LGA    I     278      I     278          3.042
LGA    A     279      A     279          0.596
LGA    F     280      F     280          3.351
LGA    V     281      V     281          1.201
LGA    A     282      A     282          2.295
LGA    D     299      D     299         27.784
LGA    I     300      I     300         21.257
LGA    D     301      D     301         19.587
LGA    L     302      L     302         12.886
LGA    L     303      L     303          6.646
LGA    V     304      V     304          1.118
LGA    A     327      A     327         15.761
LGA    A     328      A     328         15.485
LGA    A     329      A     329         16.005
LGA    I     330      I     330         18.579
LGA    P     331      P     331         20.977
LGA    L     356      L     356         10.816
LGA    R     357      R     357         11.978
LGA    V     358      V     358          9.325
LGA    G     359      G     359         13.255
LGA    A     360      A     360         19.362
LGA    M     376      M     376         10.099
LGA    S     377      S     377          9.885

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   41  191    4.0     16    2.47     7.984     6.885     0.622

LGA_LOCAL      RMSD =  2.474  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.374  Number of atoms =   41 
Std_ALL_ATOMS  RMSD =  9.110  (standard rmsd on all 41 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.659955 * X  +  -0.723745 * Y  +   0.201624 * Z  +  80.118530
  Y_new =  -0.139850 * X  +   0.145335 * Y  +   0.979449 * Z  + -12.804265
  Z_new =  -0.738174 * X  +  -0.674589 * Y  +  -0.005301 * Z  +  36.466488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.578655    1.562938  [ DEG:   -90.4503     89.5497 ]
  Theta =   0.830360    2.311232  [ DEG:    47.5761    132.4239 ]
  Phi   =  -0.208820    2.932773  [ DEG:   -11.9645    168.0355 ]
 
# 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: T0301TS464_3_1-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_1-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   41  191   4.0   16   2.47   6.885     9.11
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     23  CA  GLY   207      94.020  -2.922  14.190  1.00  0.00
ATOM     24  CA  THR   208      90.438  -1.657  14.141  1.00  0.00
ATOM     25  CA  PHE   209      91.279   2.076  14.581  1.00  0.00
ATOM     26  CA  LYS   210      94.120   1.883  12.016  1.00  0.00
ATOM     27  CA  ALA   211      91.737   0.691   9.291  1.00  0.00
ATOM     28  CA  THR   212      89.454   3.333  10.783  1.00  0.00
ATOM     29  CA  MET   213      91.860   6.150   9.890  1.00  0.00
ATOM     30  CA  ILE   214      92.447   4.679   6.391  1.00  0.00
ATOM     31  CA  ASN   215      88.696   4.794   5.591  1.00  0.00
ATOM     32  CA  ALA   216      88.855   8.458   6.595  1.00  0.00
ATOM     33  CA  GLY   217      91.851   9.367   4.422  1.00  0.00
ATOM     34  CA  ILE   218      94.056   9.763   7.515  1.00  0.00
ATOM     35  CA  PRO   219      97.660   8.577   7.640  1.00  0.00
ATOM     36  CA  THR   220      98.785   7.142  10.974  1.00  0.00
ATOM     37  CA  VAL   221     100.979   4.311  11.432  1.00  0.00
ATOM     38  CA  PHE   222     100.905   1.407  13.943  1.00  0.00
ATOM     39  CA  PRO   276     100.699  14.704   8.206  1.00  0.00
ATOM     40  CA  LYS   277     101.559  11.469  10.005  1.00  0.00
ATOM     41  CA  ILE   278      99.313  10.196  12.815  1.00  0.00
ATOM     42  CA  ALA   279     100.737   7.625  15.235  1.00  0.00
ATOM     43  CA  PHE   280      98.336   4.902  16.502  1.00  0.00
ATOM     44  CA  VAL   281      99.715   3.546  19.797  1.00  0.00
ATOM     45  CA  ALA   282      98.702  -0.084  20.381  1.00  0.00
ATOM     46  CA  ASP   299     106.608  12.780  13.519  1.00  0.00
ATOM     47  CA  ILE   300     103.048  12.258  14.548  1.00  0.00
ATOM     48  CA  ASP   301     100.205  14.372  15.962  1.00  0.00
ATOM     49  CA  LEU   302      98.328  11.986  18.236  1.00  0.00
ATOM     50  CA  LEU   303      98.438   8.464  19.525  1.00  0.00
ATOM     51  CA  VAL   304      95.686   5.997  19.986  1.00  0.00
ATOM     52  CA  ALA   327      92.535  15.364  18.535  1.00  0.00
ATOM     53  CA  ALA   328      91.100  15.615  15.020  1.00  0.00
ATOM     54  CA  ALA   329      93.263  13.606  12.587  1.00  0.00
ATOM     55  CA  ILE   330      93.336  15.115   9.045  1.00  0.00
ATOM     56  CA  PRO   331      93.946  13.599   5.559  1.00  0.00
ATOM     57  CA  LEU   356      96.677  14.502  20.561  1.00  0.00
ATOM     58  CA  ARG   357      95.440  11.752  22.801  1.00  0.00
ATOM     59  CA  VAL   358      92.394  10.015  21.279  1.00  0.00
ATOM     60  CA  GLY   359      90.432   9.775  24.496  1.00  0.00
ATOM     61  CA  ALA   360      89.283  12.047  27.344  1.00  0.00
ATOM     62  CA  MET   376      90.204   7.618  19.371  1.00  0.00
ATOM     63  CA  SER   377      87.537   6.825  16.752  1.00  0.00
TER
END
