
#######################################################
#                                                     #
#                        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   38 (   38),  selected   38 , name T0365TS464_5_2-D1
# Molecule2: number of CA atoms  207 ( 1594),  selected   38 , name T0365_D1.pdb
# PARAMETERS: T0365TS464_5_2-D1.T0365_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:    16        33 - 63          4.98    23.31
  LCS_AVERAGE:      6.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       173 - 187         1.13    22.62
  LCS_AVERAGE:      6.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       174 - 187         0.98    22.88
  LCS_AVERAGE:      5.57

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:  207
LCS_GDT     V      33     V      33     12   13   16    10   12   12   12   12   12   12   13   13   16   16   16   16   18   19   19   20   21   21   21 
LCS_GDT     P      34     P      34     12   13   16    10   12   12   12   12   12   12   13   13   14   14   14   16   18   19   19   20   21   21   21 
LCS_GDT     F      35     F      35     12   13   16    10   12   12   12   12   12   12   13   13   14   14   14   14   18   18   18   20   21   21   21 
LCS_GDT     F      36     F      36     12   13   16    10   12   12   12   12   12   15   15   15   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     E      37     E      37     12   13   16    10   12   12   12   12   14   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     A      38     A      38     12   13   16    10   12   12   12   12   12   12   13   13   14   15   16   16   18   18   19   20   21   21   21 
LCS_GDT     T      39     T      39     12   13   16    10   12   12   12   12   12   12   13   13   14   14   15   16   18   18   19   20   21   21   21 
LCS_GDT     I      40     I      40     12   13   16    10   12   12   12   12   12   12   13   13   14   14   14   16   18   18   19   20   21   21   21 
LCS_GDT     T      41     T      41     12   13   16    10   12   12   12   12   12   12   13   13   14   14   14   16   18   18   19   19   21   21   21 
LCS_GDT     G      42     G      42     12   13   16    10   12   12   12   12   12   12   13   13   14   14   14   16   18   18   18   18   20   20   20 
LCS_GDT     N      43     N      43     12   13   16     7   12   12   12   12   12   12   13   13   14   14   14   16   18   18   18   18   20   20   20 
LCS_GDT     W      44     W      44     12   13   16     7   12   12   12   12   12   12   13   13   14   14   14   16   18   18   18   18   20   20   20 
LCS_GDT     D      45     D      45      3   13   16     3    3    3    7   11   12   12   13   13   14   14   14   14   14   15   16   16   20   20   20 
LCS_GDT     D      46     D      46      3    3   16     3    3    3    4    4    6    8   10   10   14   14   14   14   14   15   16   16   16   17   17 
LCS_GDT     D      62     D      62      9    9   16     9    9    9    9    9    9    9    9    9    9    9    9   11   14   15   16   16   16   17   17 
LCS_GDT     S      63     S      63      9    9   16     9    9    9    9    9    9    9    9    9    9    9    9   11   13   15   16   16   16   17   17 
LCS_GDT     L      64     L      64      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9   14   16   17   17 
LCS_GDT     K      65     K      65      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9   11   15 
LCS_GDT     R      66     R      66      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E      67     E      67      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     I      68     I      68      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     R      69     R      69      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L      70     L      70      9    9    9     9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     173     D     173     11   15   15     4    5   11   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     D     174     D     174     14   15   15     4    4    8   12   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     L     175     L     175     14   15   15     4   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     Q     176     Q     176     14   15   15     6   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     I     177     I     177     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     Q     178     Q     178     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     L     179     L     179     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     R     180     R     180     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     R     181     R     181     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     Q     182     Q     182     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     L     183     L     183     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     F     184     F     184     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   18   19   19   20   21   21   21 
LCS_GDT     A     185     A     185     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     L     186     L     186     14   15   15     7   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_GDT     E     187     E     187     14   15   15     5   13   13   14   15   15   15   15   16   17   17   17   17   17   19   19   20   21   21   21 
LCS_AVERAGE  LCS_A:   6.19  (   5.57    6.08    6.92 )

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     10     13     13     14     15     15     15     15     16     17     17     17     17     18     19     19     20     21     21     21 
GDT PERCENT_CA   4.83   6.28   6.28   6.76   7.25   7.25   7.25   7.25   7.73   8.21   8.21   8.21   8.21   8.70   9.18   9.18   9.66  10.14  10.14  10.14
GDT RMS_LOCAL    0.32   0.56   0.56   0.95   1.13   1.13   1.13   1.13   1.78   2.16   2.16   2.16   2.16   5.07   3.44   3.44   4.39   4.76   4.76   4.60
GDT RMS_ALL_CA  21.37  22.69  22.69  22.45  22.62  22.62  22.62  22.62  22.39  22.21  22.21  22.21  22.21  17.11  21.59  21.59  22.37  22.65  22.65  21.19

#      Molecule1      Molecule2       DISTANCE
LGA    V      33      V      33          8.106
LGA    P      34      P      34         10.252
LGA    F      35      F      35         12.792
LGA    F      36      F      36          6.868
LGA    E      37      E      37          6.583
LGA    A      38      A      38         13.958
LGA    T      39      T      39         15.773
LGA    I      40      I      40         14.841
LGA    T      41      T      41         18.179
LGA    G      42      G      42         23.636
LGA    N      43      N      43         23.475
LGA    W      44      W      44         25.399
LGA    D      45      D      45         29.270
LGA    D      46      D      46         25.297
LGA    D      62      D      62         34.083
LGA    S      63      S      63         39.994
LGA    L      64      L      64         38.656
LGA    K      65      K      65         35.410
LGA    R      66      R      66         41.032
LGA    E      67      E      67         44.608
LGA    I      68      I      68         40.396
LGA    R      69      R      69         40.990
LGA    L      70      L      70         47.558
LGA    D     173      D     173          2.003
LGA    D     174      D     174          2.368
LGA    L     175      L     175          0.940
LGA    Q     176      Q     176          0.773
LGA    I     177      I     177          0.600
LGA    Q     178      Q     178          0.421
LGA    L     179      L     179          0.910
LGA    R     180      R     180          1.223
LGA    R     181      R     181          0.762
LGA    Q     182      Q     182          0.307
LGA    L     183      L     183          0.640
LGA    F     184      F     184          0.999
LGA    A     185      A     185          1.070
LGA    L     186      L     186          0.862
LGA    E     187      E     187          1.066

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   38  207    4.0     15    1.13     7.367     7.123     1.222

LGA_LOCAL      RMSD =  1.128  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 22.622  Number of atoms =   38 
Std_ALL_ATOMS  RMSD = 15.218  (standard rmsd on all 38 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.671906 * X  +   0.711819 * Y  +  -0.204589 * Z  +  58.256168
  Y_new =  -0.703642 * X  +  -0.699718 * Y  +  -0.123621 * Z  +  52.569248
  Z_new =  -0.231150 * X  +   0.060896 * Y  +   0.971011 * Z  +  48.614761 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.062632   -3.078961  [ DEG:     3.5885   -176.4115 ]
  Theta =   0.233260    2.908333  [ DEG:    13.3648    166.6352 ]
  Phi   =  -2.333127    0.808466  [ DEG:  -133.6783     46.3217 ]
 
# 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: T0365TS464_5_2-D1                             
REMARK     2: T0365_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0365TS464_5_2-D1.T0365_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   38  207   4.0   15   1.13   7.123    15.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0365TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0365
PARENT N/A
ATOM      1  CA  VAL    33      29.052  24.194  59.805  1.00  0.00
ATOM      2  CA  PRO    34      26.097  26.469  59.066  1.00  0.00
ATOM      3  CA  PHE    35      28.238  28.924  57.111  1.00  0.00
ATOM      4  CA  PHE    36      29.903  26.054  55.289  1.00  0.00
ATOM      5  CA  GLU    37      26.548  24.605  54.318  1.00  0.00
ATOM      6  CA  ALA    38      25.265  27.995  53.110  1.00  0.00
ATOM      7  CA  THR    39      28.437  28.621  51.138  1.00  0.00
ATOM      8  CA  ILE    40      28.185  25.284  49.359  1.00  0.00
ATOM      9  CA  THR    41      24.524  25.792  48.476  1.00  0.00
ATOM     10  CA  GLY    42      25.169  29.355  47.301  1.00  0.00
ATOM     11  CA  ASN    43      22.878  30.704  50.042  1.00  0.00
ATOM     12  CA  TRP    44      25.620  33.146  51.026  1.00  0.00
ATOM     13  CA  ASP    45      28.562  34.332  48.954  1.00  0.00
ATOM     14  CA  ASP    46      31.844  33.319  50.566  1.00  0.00
ATOM     15  CA  ASP    62      30.102  24.686  67.387  1.00  0.00
ATOM     16  CA  SER    63      29.272  28.097  68.809  1.00  0.00
ATOM     17  CA  LEU    64      31.732  29.547  66.349  1.00  0.00
ATOM     18  CA  LYS    65      29.940  27.652  63.588  1.00  0.00
ATOM     19  CA  ARG    66      26.527  28.655  64.964  1.00  0.00
ATOM     20  CA  GLU    67      27.415  32.321  64.891  1.00  0.00
ATOM     21  CA  ILE    68      28.536  31.939  61.298  1.00  0.00
ATOM     22  CA  ARG    69      25.335  30.118  60.296  1.00  0.00
ATOM     23  CA  LEU    70      22.717  32.512  61.683  1.00  0.00
ATOM     24  CA  ASP   173      33.801  36.439  49.595  1.00  0.00
ATOM     25  CA  ASP   174      30.988  38.753  50.676  1.00  0.00
ATOM     26  CA  LEU   175      30.745  37.095  54.110  1.00  0.00
ATOM     27  CA  GLN   176      34.322  36.029  54.895  1.00  0.00
ATOM     28  CA  ILE   177      35.320  39.113  56.891  1.00  0.00
ATOM     29  CA  GLN   178      32.525  38.423  59.126  1.00  0.00
ATOM     30  CA  LEU   179      34.315  35.099  59.541  1.00  0.00
ATOM     31  CA  ARG   180      37.578  36.897  60.408  1.00  0.00
ATOM     32  CA  ARG   181      35.888  39.255  62.860  1.00  0.00
ATOM     33  CA  GLN   182      33.988  36.321  64.430  1.00  0.00
ATOM     34  CA  LEU   183      37.185  34.278  64.646  1.00  0.00
ATOM     35  CA  PHE   184      39.066  36.787  66.829  1.00  0.00
ATOM     36  CA  ALA   185      36.362  36.490  69.435  1.00  0.00
ATOM     37  CA  LEU   186      36.967  32.768  69.941  1.00  0.00
ATOM     38  CA  GLU   187      40.703  32.203  69.538  1.00  0.00
TER
END
