
#######################################################
#                                                     #
#                        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   67 (   67),  selected   67 , name T0356TS677_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   67 , name T0356_D3.pdb
# PARAMETERS: T0356TS677_1-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:    26       348 - 373         4.57     8.93
  LCS_AVERAGE:     19.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       374 - 387         1.92    15.61
  LCS_AVERAGE:      7.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       376 - 386         0.62    14.74
  LCS_AVERAGE:      5.65

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     F     348     F     348      9   10   26     4    6   15   20   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     P     349     P     349      9   10   26     5   13   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     E     350     E     350      9   10   26     5   11   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     I     351     I     351      9   10   26     8   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     352     V     352      9   10   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     D     353     D     353      9   10   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     F     354     F     354      9   10   26     7   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     Y     355     Y     355      9   10   26     7   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     L     356     L     356      9   10   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     P     357     P     357      5   10   26     6   14   16   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     P     358     P     358      4    6   26     0    4    4    4    6    8    8    9   10   12   13   15   19   23   28   30   43   54   54   54 
LCS_GDT     E     359     E     359      4    6   26     3    4    4    5    7    8    8    9   10   12   13   16   20   28   35   45   50   54   54   54 
LCS_GDT     G     360     G     360      4    6   26     3    4    4    5    7    8    8    9   10   18   29   38   44   47   50   51   52   56   60   60 
LCS_GDT     C     361     C     361      4    6   26     3    4    4    5    7    8    9   25   32   36   40   42   47   49   50   53   57   59   60   61 
LCS_GDT     S     362     S     362      4    6   26     3    4    4    5    7   12   15   31   33   36   40   42   47   49   50   53   57   59   60   61 
LCS_GDT     Y     363     Y     363      3   11   26     3    4    4    6   17   28   30   32   34   36   40   42   47   49   50   55   57   59   60   62 
LCS_GDT     R     364     R     364      8   11   26     5   10   16   20   25   27   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     L     365     L     365      8   11   26     5   14   17   21   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     A     366     A     366      8   11   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     367     V     367      8   11   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     368     V     368      8   11   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     T     369     T     369      8   11   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     I     370     I     370      8   11   26     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     K     371     K     371      8   11   26     3   10   16   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     K     372     K     372      7   11   26     3    4    7   13   23   28   30   32   34   36   37   42   47   49   52   56   58   59   60   62 
LCS_GDT     Q     373     Q     373      7   11   26     4   11   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     Y     374     Y     374      4   14   24     0    4    6   10   13   14   16   20   24   26   30   35   41   47   52   56   58   59   60   62 
LCS_GDT     A     375     A     375      4   14   24     3    4    4    9   12   14   16   20   24   26   29   34   36   42   50   54   58   59   60   62 
LCS_GDT     G     376     G     376     11   14   24     3    9   11   11   13   14   16   21   25   31   36   40   44   48   52   56   58   59   60   62 
LCS_GDT     H     377     H     377     11   14   24     8   10   11   11   13   15   19   26   32   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     A     378     A     378     11   14   25     8   10   11   11   13   14   18   26   32   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     K     379     K     379     11   14   25     8   10   11   11   13   15   18   25   32   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     R     380     R     380     11   14   25     8   10   11   11   13   14   19   26   32   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     381     V     381     11   14   25     8   10   11   11   13   14   16   26   32   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     M     382     M     382     11   14   25     8   10   11   11   13   14   16   24   29   33   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     M     383     M     383     11   14   25     8   10   11   11   13   14   18   26   32   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     G     384     G     384     11   14   25     7   10   11   11   13   14   16   20   29   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     385     V     385     11   14   25     8   10   11   11   13   14   16   20   24   26   30   37   44   47   51   56   58   59   60   62 
LCS_GDT     W     386     W     386     11   14   25     4   10   11   11   13   14   18   23   29   33   39   42   44   47   51   56   58   59   60   62 
LCS_GDT     S     387     S     387      4   14   25     3    4    7    8   12   12   18   25   32   36   40   42   46   49   52   56   58   59   60   62 
LCS_GDT     F     388     F     388      4    5   25     3    4    4    4    7    9   11   14   20   26   34   42   47   49   52   56   58   59   60   62 
LCS_GDT     L     389     L     389      4    5   25     3    4    4    4    5    7   10   17   20   29   37   42   47   49   52   56   58   59   60   62 
LCS_GDT     R     390     R     390      4    5   25     3   10   11   14   16   22   29   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     Q     391     Q     391      3    4   25     3    8   15   22   24   28   30   32   34   36   37   41   47   49   52   56   58   59   60   62 
LCS_GDT     F     392     F     392      3    4   25     3   10   15   22   24   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     M     393     M     393      3    4   25     3    3    5   13   17   23   29   32   34   36   37   42   47   49   52   56   58   59   60   62 
LCS_GDT     K     396     K     396      3    9   25     3    3   16   21   25   27   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     F     397     F     397      8    9   25     6   14   17   21   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     398     V     398      8    9   25     8   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     I     399     I     399      8    9   25     9   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     V     400     V     400      8    9   25     6   14   17   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     C     401     C     401      8    9   25     6   14   15   22   25   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     D     402     D     402      8    9   25     6   14   15   18   24   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     D     403     D     403      8    9   25     0    4    4   16   17   20   29   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     N     406     N     406      8    9   25     0    7   15   16   24   28   30   32   34   36   40   42   47   49   52   56   58   59   60   62 
LCS_GDT     A     407     A     407      3    5   19     2    3    4    5    6    6    8   19   33   35   37   40   47   49   52   56   58   59   60   62 
LCS_GDT     R     408     R     408      3    5   19     3    3    4    5    6    6    8   15   19   32   36   39   44   49   52   56   58   59   60   62 
LCS_GDT     D     409     D     409      3    4   19     3    3    3    4    4    6   12   13   16   29   32   36   41   48   52   56   58   59   60   62 
LCS_GDT     W     410     W     410      3    4   17     3    3    3    3    4    6    7   12   15   17   22   24   33   34   40   42   53   54   60   62 
LCS_GDT     N     411     N     411      3    4   17     3    3    5   10   12   14   16   20   21   23   25   29   33   36   42   52   58   59   60   62 
LCS_GDT     D     412     D     412      3    4   17     3    3    3    5    5    6   10   13   21   24   25   28   33   43   50   56   58   59   60   62 
LCS_GDT     V     413     V     413      3    6   17     3    3    4    5    6    9   16   20   24   29   33   35   41   48   52   56   58   59   60   62 
LCS_GDT     I     414     I     414      5    6   17     5    5    5    5   12   14   16   21   24   29   33   35   41   48   52   56   58   59   60   62 
LCS_GDT     W     415     W     415      5    6   17     5    5    5    5   11   14   14   20   21   24   25   27   33   36   40   43   47   53   59   62 
LCS_GDT     A     416     A     416      5    6   17     5    5    5    5    5    6    8    9   10   14   16   21   28   31   40   43   45   53   59   62 
LCS_GDT     I     417     I     417      5    6   17     5    5    5    5    7   11   16   21   24   29   32   36   41   47   52   56   58   59   60   62 
LCS_GDT     T     418     T     418      5    6   17     5    5    5    8   13   14   16   20   24   26   29   34   36   45   50   56   58   59   60   62 
LCS_AVERAGE  LCS_A:  11.10  (   5.65    7.67   19.99 )

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      9     14     17     22     25     28     30     32     34     36     40     42     47     49     52     56     58     59     60     62 
GDT PERCENT_CA   7.50  11.67  14.17  18.33  20.83  23.33  25.00  26.67  28.33  30.00  33.33  35.00  39.17  40.83  43.33  46.67  48.33  49.17  50.00  51.67
GDT RMS_LOCAL    0.36   0.65   0.85   1.32   1.47   1.85   1.94   2.17   2.46   2.76   3.91   3.98   4.42   4.59   5.41   5.81   6.03   5.97   6.06   6.45
GDT RMS_ALL_CA   8.58   8.64   8.64   8.57   8.37   8.45   8.36   8.37   8.35   8.36   8.40   8.36   8.15   8.08   7.60   7.50   7.55   7.37   7.37   7.54

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348          2.705
LGA    P     349      P     349          1.151
LGA    E     350      E     350          2.333
LGA    I     351      I     351          1.235
LGA    V     352      V     352          2.165
LGA    D     353      D     353          2.204
LGA    F     354      F     354          1.977
LGA    Y     355      Y     355          1.488
LGA    L     356      L     356          1.301
LGA    P     357      P     357          2.237
LGA    P     358      P     358         15.742
LGA    E     359      E     359         16.065
LGA    G     360      G     360         11.556
LGA    C     361      C     361          6.477
LGA    S     362      S     362          5.959
LGA    Y     363      Y     363          3.479
LGA    R     364      R     364          3.790
LGA    L     365      L     365          2.751
LGA    A     366      A     366          1.526
LGA    V     367      V     367          1.228
LGA    V     368      V     368          1.279
LGA    T     369      T     369          1.772
LGA    I     370      I     370          2.098
LGA    K     371      K     371          1.793
LGA    K     372      K     372          2.911
LGA    Q     373      Q     373          0.694
LGA    Y     374      Y     374         12.218
LGA    A     375      A     375         14.280
LGA    G     376      G     376         12.975
LGA    H     377      H     377         10.365
LGA    A     378      A     378          9.478
LGA    K     379      K     379         10.707
LGA    R     380      R     380         10.030
LGA    V     381      V     381          8.830
LGA    M     382      M     382         10.593
LGA    M     383      M     383         10.626
LGA    G     384      G     384          9.915
LGA    V     385      V     385         10.867
LGA    W     386      W     386         11.831
LGA    S     387      S     387         11.783
LGA    F     388      F     388         10.876
LGA    L     389      L     389          9.428
LGA    R     390      R     390          5.502
LGA    Q     391      Q     391          2.106
LGA    F     392      F     392          1.679
LGA    M     393      M     393          3.673
LGA    K     396      K     396          2.743
LGA    F     397      F     397          3.409
LGA    V     398      V     398          2.282
LGA    I     399      I     399          1.964
LGA    V     400      V     400          0.900
LGA    C     401      C     401          1.481
LGA    D     402      D     402          2.740
LGA    D     403      D     403          4.996
LGA    N     406      N     406          3.183
LGA    A     407      A     407          5.374
LGA    R     408      R     408          6.593
LGA    D     409      D     409          9.072
LGA    W     410      W     410         14.731
LGA    N     411      N     411         13.924
LGA    D     412      D     412         12.658
LGA    V     413      V     413         10.617
LGA    I     414      I     414         11.063
LGA    W     415      W     415         14.959
LGA    A     416      A     416         14.864
LGA    I     417      I     417         10.806
LGA    T     418      T     418         13.447

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67  120    4.0     32    2.17    25.833    21.374     1.409

LGA_LOCAL      RMSD =  2.171  Number of atoms =   32  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.269  Number of atoms =   67 
Std_ALL_ATOMS  RMSD =  7.238  (standard rmsd on all 67 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.671839 * X  +   0.051277 * Y  +  -0.738920 * Z  +  45.889111
  Y_new =  -0.293575 * X  +  -0.897463 * Y  +  -0.329201 * Z  + 115.441704
  Z_new =  -0.680034 * X  +   0.438098 * Y  +  -0.587897 * Z  +  83.036835 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.501173   -0.640419  [ DEG:   143.3067    -36.6933 ]
  Theta =   0.747809    2.393783  [ DEG:    42.8463    137.1537 ]
  Phi   =  -0.411967    2.729626  [ DEG:   -23.6040    156.3960 ]
 
# 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: T0356TS677_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS677_1-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   67  120   4.0   32   2.17  21.374     7.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS677_1-D3
PFRMAT TS
TARGET T0356
MODEL  1
PARENT 2D1Q_A
ATOM    463  CA  PHE   348      58.728  71.097  53.705  1.00 99.00
ATOM    464  CA  PRO   349      57.341  72.742  50.511  1.00 38.00
ATOM    465  CA  GLU   350      54.297  70.399  50.393  1.00 45.00
ATOM    466  CA  ILE   351      53.357  70.859  54.076  1.00 62.00
ATOM    467  CA  VAL   352      51.201  73.805  55.049  1.00 47.00
ATOM    468  CA  ASP   353      50.727  72.998  58.750  1.00 27.00
ATOM    469  CA  PHE   354      51.745  70.240  61.173  1.00 40.00
ATOM    470  CA  TYR   355      51.306  69.136  64.778  1.00 29.00
ATOM    471  CA  LEU   356      53.143  66.492  66.813  1.00 27.00
ATOM    472  CA  PRO   357      52.247  64.413  69.903  1.00 47.00
ATOM    477  CA  PRO   358      53.953  49.102  75.224  1.00 50.00
ATOM    478  CA  GLU   359      57.684  48.866  74.326  1.00 63.00
ATOM    479  CA  GLY   360      58.901  52.472  74.196  1.00 60.00
ATOM    480  CA  CYS   361      56.320  54.302  76.358  1.00 47.00
ATOM    481  CA  SER   362      55.610  56.989  73.738  1.00 57.00
ATOM    482  CA  TYR   363      56.194  57.321  69.956  1.00 58.00
ATOM    483  CA  ARG   364      56.300  60.645  68.086  1.00 41.00
ATOM    484  CA  LEU   365      53.488  60.915  65.575  1.00 55.00
ATOM    485  CA  ALA   366      52.226  63.779  63.428  1.00 60.00
ATOM    486  CA  VAL   367      49.146  65.302  61.851  1.00 49.00
ATOM    487  CA  VAL   368      49.926  67.013  58.542  1.00 54.00
ATOM    488  CA  THR   369      48.040  69.510  56.352  1.00 55.00
ATOM    489  CA  ILE   370      49.300  69.555  52.757  1.00 55.00
ATOM    490  CA  LYS   371      49.324  72.609  50.469  1.00 70.00
ATOM    491  CA  LYS   372      46.244  72.572  48.198  1.00 92.00
ATOM    492  CA  GLN   373      46.867  70.396  45.126  1.00 99.00
ATOM    496  CA  TYR   374      52.205  59.553  51.447  1.00 99.00
ATOM    497  CA  ALA   375      52.676  58.629  55.129  1.00 99.00
ATOM    498  CA  GLY   376      56.042  57.034  54.252  1.00 99.00
ATOM    499  CA  HIS   377      57.273  60.057  52.253  1.00 99.00
ATOM    500  CA  ALA   378      56.743  62.317  55.276  1.00 99.00
ATOM    501  CA  LYS   379      58.470  59.741  57.545  1.00 99.00
ATOM    502  CA  ARG   380      61.463  59.315  55.168  1.00 99.00
ATOM    503  CA  VAL   381      61.974  63.093  54.865  1.00 99.00
ATOM    504  CA  MET   382      61.941  63.499  58.693  1.00 99.00
ATOM    505  CA  MET   383      64.320  60.537  59.170  1.00 99.00
ATOM    506  CA  GLY   384      66.872  62.133  56.824  1.00 86.00
ATOM    507  CA  VAL   385      66.971  65.361  58.897  1.00 83.00
ATOM    508  CA  TRP   386      66.843  64.322  62.585  1.00 99.00
ATOM    509  CA  SER   387      68.550  61.830  64.896  1.00 99.00
ATOM    510  CA  PHE   388      67.209  58.305  65.481  1.00 99.00
ATOM    511  CA  LEU   389      65.146  59.118  68.596  1.00 99.00
ATOM    512  CA  ARG   390      63.146  61.916  66.920  1.00 99.00
ATOM    513  CA  GLN   391      61.841  59.670  64.064  1.00 99.00
ATOM    514  CA  PHE   392      58.076  59.582  63.533  1.00 99.00
ATOM    515  CA  MET   393      57.630  55.995  64.694  1.00 99.00
ATOM    516  CA  LYS   396      54.039  56.745  65.732  1.00 99.00
ATOM    517  CA  PHE   397      52.781  57.415  62.200  1.00 99.00
ATOM    518  CA  VAL   398      51.515  60.309  60.084  1.00 99.00
ATOM    519  CA  ILE   399      47.884  61.259  59.427  1.00 99.00
ATOM    520  CA  VAL   400      46.692  63.816  56.901  1.00 99.00
ATOM    521  CA  CYS   401      44.034  66.283  58.096  1.00 99.00
ATOM    522  CA  ASP   402      42.165  69.437  56.965  1.00 99.00
ATOM    523  CA  ASP   403      43.133  71.392  60.099  1.00 99.00
ATOM    525  CA  ASN   406      43.909  71.182  66.151  1.00 87.00
ATOM    526  CA  ALA   407      45.199  74.367  67.835  1.00 81.00
ATOM    527  CA  ARG   408      44.249  76.886  70.495  1.00 53.00
ATOM    528  CA  ASP   409      43.499  80.502  69.683  1.00 53.00
ATOM    529  CA  TRP   410      47.075  81.701  70.258  1.00 38.00
ATOM    530  CA  ASN   411      48.675  78.895  68.282  1.00 54.00
ATOM    531  CA  ASP   412      49.289  76.168  70.880  1.00 75.00
ATOM    532  CA  VAL   413      48.896  72.590  69.621  1.00 85.00
ATOM    533  CA  ILE   414      46.132  70.502  71.196  1.00 77.00
ATOM    534  CA  TRP   415      48.233  67.409  71.967  1.00 99.00
ATOM    535  CA  ALA   416      45.153  65.567  73.339  1.00 93.00
ATOM    536  CA  ILE   417      43.211  66.045  70.103  1.00 93.00
ATOM    537  CA  THR   418      46.214  64.783  68.038  1.00 93.00
TER
END
