
#######################################################
#                                                     #
#                        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   62 (   62),  selected   62 , name T0356TS464_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   62 , name T0356_D2.pdb
# PARAMETERS: T0356TS464_3-D2.T0356_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:    18       242 - 259         4.92    21.74
  LONGEST_CONTINUOUS_SEGMENT:    18       256 - 273         4.56    27.44
  LONGEST_CONTINUOUS_SEGMENT:    18       257 - 274         4.88    27.91
  LCS_AVERAGE:      7.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       242 - 249         0.54    30.93
  LCS_AVERAGE:      2.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       242 - 249         0.54    30.93
  LCS_AVERAGE:      2.28

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:  192
LCS_GDT     T     122     T     122      3    3   11     3    3    3    4    4    4    4    6    8    8   10   10   10   10   10   13   14   14   14   18 
LCS_GDT     K     123     K     123      3    3   12     3    3    3    4    4    5    5    6    8    9   10   10   11   14   14   16   16   17   17   18 
LCS_GDT     R     124     R     124      3    3   13     3    3    3    4    4    5    6    7    9   10   12   13   13   14   14   16   16   17   17   18 
LCS_GDT     L     125     L     125      4    4   13     3    3    4    4    4    5    6    7    8    9   10   13   13   14   14   16   16   17   17   18 
LCS_GDT     R     126     R     126      4    4   13     3    3    4    4    4    4    6    6    8   10   12   13   13   14   14   16   16   17   17   18 
LCS_GDT     G     127     G     127      4    5   13     3    3    4    5    8    9    9    9   10   10   12   13   13   14   14   16   16   17   17   18 
LCS_GDT     A     128     A     128      4    5   13     0    3    4    4    8    9    9    9   10   10   12   13   13   13   14   16   16   17   17   18 
LCS_GDT     P     129     P     129      3    5   13     1    3    4    4    8    9    9    9   10   10   12   13   13   13   14   14   16   16   17   18 
LCS_GDT     C     130     C     130      3    5   13     3    3    4    5    8    9    9    9   10   10   12   13   13   13   14   16   16   17   17   18 
LCS_GDT     Q     131     Q     131      3    5   13     3    3    4    4    5    5    6    7   10   10   12   13   13   14   14   16   16   17   17   18 
LCS_GDT     Q     132     Q     132      5    5   13     3    5    5    5    7    9    9    9   10   10   12   13   13   14   14   16   16   17   17   18 
LCS_GDT     K     133     K     133      5    5   13     3    5    5    5    8    9    9    9   10   10   12   13   13   14   14   16   16   17   18   20 
LCS_GDT     I     134     I     134      5    5   13     3    5    5    5    8    9    9    9   10   10   12   13   13   14   14   16   16   17   17   18 
LCS_GDT     V     135     V     135      5    5   13     3    5    5    5    8    9    9    9   10   10   12   13   13   13   14   14   15   16   17   17 
LCS_GDT     S     136     S     136      5    5   13     3    5    5    5    8    9    9    9   10   10   12   13   13   13   14   14   14   16   16   17 
LCS_GDT     G     177     G     177      3    5   13     2    3    5    5    5    5    6    7    7    9   10   10   10   13   14   14   15   16   16   17 
LCS_GDT     I     178     I     178      4    5   13     4    4    5    5    5    5    6    7    8   10   10   10   12   13   14   16   19   20   24   26 
LCS_GDT     Y     179     Y     179      4    5   13     4    4    5    5    5    6    8   10   11   12   14   17   18   19   20   22   24   24   25   26 
LCS_GDT     R     180     R     180      4    5   13     4    4    5    5    5    5    6    8   11   12   14   17   18   19   20   21   23   24   25   26 
LCS_GDT     Q     181     Q     181      4    5   13     4    4    5    5    5    5    6   11   12   14   15   17   18   18   18   20   21   23   23   26 
LCS_GDT     V     219     V     219      3    3    8     3    3    3    3    3    3    6    7    8    8    8    8    8    9   12   13   18   18   18   18 
LCS_GDT     A     220     A     220      3    7    8     3    3    4    4    6    6    7    7    8    8    8    8    9   10   12   15   18   18   18   18 
LCS_GDT     L     221     L     221      5    7    8     3    4    5    6    6    6    7    9    9   10   11   12   17   19   20   23   23   25   25   25 
LCS_GDT     G     222     G     222      5    7    8     3    4    5    6    6    6    7    9   10   12   13   15   18   20   22   23   24   25   25   26 
LCS_GDT     A     223     A     223      5    7    8     3    4    5    6    6    6    7    9    9    9   11   12   14   17   19   23   24   24   25   26 
LCS_GDT     D     224     D     224      5    7    8     3    4    5    6    6    6    7    9    9    9   10   11   13   14   14   18   19   21   23   26 
LCS_GDT     P     225     P     225      5    7    8     3    4    5    6    6    6    7    9    9    9   10   11   13   14   14   16   16   17   17   23 
LCS_GDT     A     226     A     226      0    7    8     0    4    4    6    6    6    7    9    9    9   10   11   13   14   14   16   16   17   17   18 
LCS_GDT     Y     242     Y     242      8    8   18     5    8    8    8    8    8    9   12   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     A     243     A     243      8    8   18     5    8    8    8    8   10   11   13   14   16   17   17   19   20   22   23   24   25   25   26 
LCS_GDT     F     244     F     244      8    8   18     6    8    8    8    8   10   11   13   14   16   17   17   19   20   22   23   24   25   25   27 
LCS_GDT     A     245     A     245      8    8   18     6    8    8    8    8    9   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     G     246     G     246      8    8   18     6    8    8    8    8   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     L     247     L     247      8    8   18     6    8    8    8    8   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     L     248     L     248      8    8   18     6    8    8    8    8   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     R     249     R     249      8    8   18     6    8    8    8    8   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     G     250     G     250      4    6   18     3    4    4    5    6    8   11   13   14   16   17   17   18   19   22   23   24   25   27   29 
LCS_GDT     T     251     T     251      4    6   18     3    4    4    6    7   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     K     252     K     252      4    6   18     3    4    5    6    7   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     T     253     T     253      4    4   18     3    4    4    4    6    7   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     E     254     E     254      3    3   18     3    3    4    6    6   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     V     255     V     255      3    3   18     3    3    3    5    6    8   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     V     256     V     256      3    3   18     0    3    3    5    6    7    9   12   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     K     257     K     257      3    3   18     1    3    3    3    6    7    9   11   12   15   16   17   19   20   22   23   24   25   27   29 
LCS_GDT     C     258     C     258      4    5   18     4    4    4    5    5    8    9   11   12   14   15   17   19   20   22   23   24   25   27   29 
LCS_GDT     I     259     I     259      4    5   18     4    4    4    5    5    5    9   11   12   14   15   17   18   18   19   20   21   25   27   29 
LCS_GDT     S     260     S     260      4    5   18     4    4    4    5    5    5    6    7    8   11   11   17   18   18   18   21   23   25   27   29 
LCS_GDT     N     261     N     261      4    5   18     4    4    4    5    6    7    9   11   12   14   15   17   19   20   22   23   24   25   27   29 
LCS_GDT     D     262     D     262      3    6   18     3    3    4    5    6    8    9   11   12   14   16   17   19   20   22   23   24   25   27   29 
LCS_GDT     L     263     L     263      5    6   18     3    5    5    6    6    9   11   13   14   15   16   17   19   20   22   23   24   25   27   29 
LCS_GDT     E     264     E     264      5    6   18     3    5    5    6    7   10   11   13   14   16   17   17   19   20   22   23   24   25   27   29 
LCS_GDT     V     265     V     265      5    6   18     3    5    5    6    6    8   11   12   14   15   17   17   18   18   19   21   23   25   27   29 
LCS_GDT     P     266     P     266      5    6   18     4    5    5    6    6    8    9   11   12   14   15   17   18   18   19   21   23   25   27   29 
LCS_GDT     A     267     A     267      5    6   18     4    5    5    6    6    7    9   11   12   14   15   17   18   18   19   21   23   25   27   29 
LCS_GDT     S     268     S     268      4    5   18     4    4    4    4    4    5    7    8    8   11   15   16   18   18   19   21   23   25   27   29 
LCS_GDT     A     269     A     269      4    5   18     4    4    4    4    5    6    8   12   12   14   15   17   18   18   19   21   23   25   27   29 
LCS_GDT     E     270     E     270      3    5   18     3    3    4    4    5    6    7   11   12   14   15   17   18   18   19   21   23   25   27   29 
LCS_GDT     I     271     I     271      3    4   18     3    3    4    4    6    8    9   11   12   14   15   17   18   18   19   21   23   25   27   29 
LCS_GDT     V     272     V     272      3    4   18     0    3    4    4    6    8    9   11   12   14   15   17   18   18   18   21   22   24   27   29 
LCS_GDT     L     273     L     273      3    3   18     1    3    3    4    4    5    9   10   11   14   15   17   18   18   18   19   20   20   21   23 
LCS_GDT     E     274     E     274      3    3   18     0    3    3    3    4    5    6    8    8    9    9   12   14   16   18   19   20   20   21   21 
LCS_GDT     G     275     G     275      3    3   11     0    3    3    3    3    3    5    5    7    9    9   10   14   16   18   19   19   19   21   21 
LCS_AVERAGE  LCS_A:   4.28  (   2.28    2.77    7.78 )

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      8      8      8      8     10     11     13     14     16     17     17     19     20     22     23     24     25     27     29 
GDT PERCENT_CA   3.12   4.17   4.17   4.17   4.17   5.21   5.73   6.77   7.29   8.33   8.85   8.85   9.90  10.42  11.46  11.98  12.50  13.02  14.06  15.10
GDT RMS_LOCAL    0.31   0.54   0.54   0.54   0.54   2.38   2.54   2.83   2.98   3.44   3.61   3.61   4.36   4.53   4.94   5.23   5.74   5.71   7.24   7.51
GDT RMS_ALL_CA  30.56  30.93  30.93  30.93  30.93  22.82  22.83  23.28  22.93  22.80  23.32  23.32  22.16  22.30  21.83  21.66  20.65  21.96  24.67  24.17

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122         33.692
LGA    K     123      K     123         37.151
LGA    R     124      R     124         41.052
LGA    L     125      L     125         42.780
LGA    R     126      R     126         44.759
LGA    G     127      G     127         45.902
LGA    A     128      A     128         44.824
LGA    P     129      P     129         44.110
LGA    C     130      C     130         39.197
LGA    Q     131      Q     131         42.619
LGA    Q     132      Q     132         41.524
LGA    K     133      K     133         38.365
LGA    I     134      I     134         38.523
LGA    V     135      V     135         36.553
LGA    S     136      S     136         37.925
LGA    G     177      G     177         21.658
LGA    I     178      I     178         19.039
LGA    Y     179      Y     179         17.284
LGA    R     180      R     180         19.451
LGA    Q     181      Q     181         22.441
LGA    V     219      V     219         27.629
LGA    A     220      A     220         23.868
LGA    L     221      L     221         17.278
LGA    G     222      G     222         14.986
LGA    A     223      A     223         13.276
LGA    D     224      D     224         13.414
LGA    P     225      P     225         13.743
LGA    A     226      A     226         19.519
LGA    Y     242      Y     242          6.640
LGA    A     243      A     243          3.362
LGA    F     244      F     244          1.473
LGA    A     245      A     245          3.434
LGA    G     246      G     246          3.402
LGA    L     247      L     247          2.977
LGA    L     248      L     248          1.957
LGA    R     249      R     249          1.673
LGA    G     250      G     250          3.927
LGA    T     251      T     251          2.255
LGA    K     252      K     252          1.979
LGA    T     253      T     253          3.863
LGA    E     254      E     254          2.819
LGA    V     255      V     255          4.968
LGA    V     256      V     256          5.263
LGA    K     257      K     257          8.403
LGA    C     258      C     258         11.265
LGA    I     259      I     259         12.814
LGA    S     260      S     260         11.695
LGA    N     261      N     261         12.787
LGA    D     262      D     262         12.437
LGA    L     263      L     263          6.289
LGA    E     264      E     264          2.597
LGA    V     265      V     265          6.120
LGA    P     266      P     266          9.859
LGA    A     267      A     267         13.651
LGA    S     268      S     268         15.959
LGA    A     269      A     269         12.515
LGA    E     270      E     270         19.318
LGA    I     271      I     271         20.971
LGA    V     272      V     272         16.828
LGA    L     273      L     273         20.139
LGA    E     274      E     274         22.301
LGA    G     275      G     275         24.316

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   62  192    4.0     13    2.83     6.771     5.659     0.444

LGA_LOCAL      RMSD =  2.828  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.445  Number of atoms =   62 
Std_ALL_ATOMS  RMSD = 17.313  (standard rmsd on all 62 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.948730 * X  +   0.074579 * Y  +  -0.307162 * Z  + -24.272253
  Y_new =  -0.232203 * X  +   0.823767 * Y  +  -0.517194 * Z  +  39.502384
  Z_new =   0.214458 * X  +   0.562002 * Y  +   0.798850 * Z  +  28.890898 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.613080   -2.528512  [ DEG:    35.1269   -144.8731 ]
  Theta =  -0.216137   -2.925456  [ DEG:   -12.3837   -167.6163 ]
  Phi   =  -0.240033    2.901560  [ DEG:   -13.7528    166.2471 ]
 
# 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_3-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_3-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   62  192   4.0   13   2.83   5.659    17.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_3-D2
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM     68  CA  THR   122      54.259  64.558  79.022  1.00  0.00
ATOM     69  CA  LYS   123      54.438  60.820  78.032  1.00  0.00
ATOM     70  CA  ARG   124      51.184  59.940  79.890  1.00  0.00
ATOM     71  CA  LEU   125      49.423  62.971  78.152  1.00  0.00
ATOM     72  CA  ARG   126      50.808  61.904  74.688  1.00  0.00
ATOM     73  CA  GLY   127      49.589  58.259  75.273  1.00  0.00
ATOM     74  CA  ALA   128      46.098  59.709  76.203  1.00  0.00
ATOM     75  CA  PRO   129      45.723  61.770  72.975  1.00  0.00
ATOM     76  CA  CYS   130      47.695  65.028  73.248  1.00  0.00
ATOM     77  CA  GLN   131      49.287  65.665  69.827  1.00  0.00
ATOM     78  CA  GLN   132      51.996  68.353  70.241  1.00  0.00
ATOM     79  CA  LYS   133      54.016  69.348  73.371  1.00  0.00
ATOM     80  CA  ILE   134      54.146  72.834  74.967  1.00  0.00
ATOM     81  CA  VAL   135      56.714  73.506  77.683  1.00  0.00
ATOM     82  CA  SER   136      56.186  75.762  80.682  1.00  0.00
ATOM     83  CA  GLY   177      56.283  60.782  63.691  1.00  0.00
ATOM     84  CA  ILE   178      59.753  62.236  63.024  1.00  0.00
ATOM     85  CA  TYR   179      63.046  62.467  65.087  1.00  0.00
ATOM     86  CA  ARG   180      65.243  65.464  65.765  1.00  0.00
ATOM     87  CA  GLN   181      68.626  63.858  64.916  1.00  0.00
ATOM     88  CA  VAL   219      58.892  81.573  87.556  1.00  0.00
ATOM     89  CA  ALA   220      62.030  83.680  87.785  1.00  0.00
ATOM     90  CA  LEU   221      64.594  81.172  86.602  1.00  0.00
ATOM     91  CA  GLY   222      61.341  79.369  85.181  1.00  0.00
ATOM     92  CA  ALA   223      63.052  76.082  86.123  1.00  0.00
ATOM     93  CA  ASP   224      61.710  72.943  84.408  1.00  0.00
ATOM     94  CA  PRO   225      60.727  71.122  87.618  1.00  0.00
ATOM     95  CA  ALA   226      61.391  70.870  91.347  1.00  0.00
ATOM     96  CA  TYR   242      81.524  76.048  67.599  1.00  0.00
ATOM     97  CA  ALA   243      78.166  74.797  66.262  1.00  0.00
ATOM     98  CA  PHE   244      76.873  74.026  69.776  1.00  0.00
ATOM     99  CA  ALA   245      78.053  77.340  71.158  1.00  0.00
ATOM    100  CA  GLY   246      76.432  79.513  68.485  1.00  0.00
ATOM    101  CA  LEU   247      73.308  77.335  68.544  1.00  0.00
ATOM    102  CA  LEU   248      72.909  77.878  72.311  1.00  0.00
ATOM    103  CA  ARG   249      73.810  81.585  72.302  1.00  0.00
ATOM    104  CA  GLY   250      77.009  80.857  74.294  1.00  0.00
ATOM    105  CA  THR   251      80.737  81.070  73.713  1.00  0.00
ATOM    106  CA  LYS   252      82.896  78.054  73.029  1.00  0.00
ATOM    107  CA  THR   253      84.483  78.590  76.447  1.00  0.00
ATOM    108  CA  GLU   254      81.038  78.023  77.997  1.00  0.00
ATOM    109  CA  VAL   255      80.774  74.717  76.096  1.00  0.00
ATOM    110  CA  VAL   256      84.327  74.265  77.511  1.00  0.00
ATOM    111  CA  LYS   257      83.704  74.939  81.167  1.00  0.00
ATOM    112  CA  CYS   258      80.251  73.280  80.944  1.00  0.00
ATOM    113  CA  ILE   259      81.646  70.274  79.115  1.00  0.00
ATOM    114  CA  SER   260      84.439  69.879  81.686  1.00  0.00
ATOM    115  CA  ASN   261      82.089  70.331  84.638  1.00  0.00
ATOM    116  CA  ASP   262      80.010  67.380  83.469  1.00  0.00
ATOM    117  CA  LEU   263      82.880  65.059  82.772  1.00  0.00
ATOM    118  CA  GLU   264      84.507  65.627  79.426  1.00  0.00
ATOM    119  CA  VAL   265      88.236  65.763  79.183  1.00  0.00
ATOM    120  CA  PRO   266      89.900  68.566  77.275  1.00  0.00
ATOM    121  CA  ALA   267      89.905  66.708  73.970  1.00  0.00
ATOM    122  CA  SER   268      86.318  65.535  74.134  1.00  0.00
ATOM    123  CA  ALA   269      85.289  69.022  75.277  1.00  0.00
ATOM    124  CA  GLU   270      87.108  70.597  72.330  1.00  0.00
ATOM    125  CA  ILE   271      85.674  68.067  69.910  1.00  0.00
ATOM    126  CA  VAL   272      82.135  69.061  70.994  1.00  0.00
ATOM    127  CA  LEU   273      82.918  72.767  70.661  1.00  0.00
ATOM    128  CA  GLU   274      84.252  72.081  67.191  1.00  0.00
ATOM    129  CA  GLY   275      81.038  70.284  66.166  1.00  0.00
TER
END
