
#######################################################
#                                                     #
#                        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   32 (   32),  selected   32 , name T0369TS464_1_2
# Molecule2: number of CA atoms  147 ( 1193),  selected   32 , name T0369.pdb
# PARAMETERS: T0369TS464_1_2.T0369.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:    20       107 - 126         4.94    16.84
  LCS_AVERAGE:     11.01

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       113 - 126         1.92    21.11
  LCS_AVERAGE:      6.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       116 - 126         0.51    21.40
  LCS_AVERAGE:      4.38

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:  147
LCS_GDT     Q      27     Q      27      3    3    9     3    3    3    3    3    4    6    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     P      28     P      28      3    3    9     3    3    3    3    3    5    6    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     E      29     E      29      3    5    9     3    3    3    3    4    5    6    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     D      30     D      30      4    6    9     4    4    4    4    5    6    7    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     W      31     W      31      4    6    9     4    4    4    4    5    6    7    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     D      32     D      32      4    6    9     4    4    4    5    5    6    7    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     K      33     K      33      4    6    9     4    4    4    5    5    6    7    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     R      34     R      34      4    6    9     3    4    4    5    5    6    7    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     P      35     P      35      4    6    9     3    4    4    5    5    6    7    7    8    8    8    8    8    9    9   10   10   12   13   14 
LCS_GDT     I      36     I      36      4    5    9     3    4    4    5    5    6    7    7    8    8    8    8    8    8    9    9    9   11   13   14 
LCS_GDT     S      37     S      37      3    3    9     3    3    3    3    3    6    6    7    8    8    8    8    8    8    9    9    9    9   12   12 
LCS_GDT     Y     106     Y     106      3    6   19     0    0    3    4    4    6    6    6   11   12   15   15   16   16   17   18   20   20   20   20 
LCS_GDT     W     107     W     107      5    8   20     3    3    5    6    7    8    9   11   12   14   15   16   17   18   19   19   20   20   20   20 
LCS_GDT     G     108     G     108      5    8   20     4    4    5    6    6    8    9   10   12   14   15   15   17   17   19   19   20   20   20   20 
LCS_GDT     V     109     V     109      5    8   20     4    4    5    6    7    8    9   11   12   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     T     110     T     110      5    8   20     4    4    5    6    7    8    9   11   12   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     D     111     D     111      5    8   20     4    5    5    6    7    8    9   11   12   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     S     112     S     112      5    8   20     3    5    5    6    7    8    9   11   12   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     T     113     T     113      4   14   20     3    5    5    6    7   12   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     T     114     T     114      4   14   20     4    5    6    9   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     G     115     G     115      4   14   20     4    4    4    8   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     W     116     W     116     11   14   20     5   11   11   11   13   13   13   14   14   14   15   18   18   18   19   19   20   20   20   20 
LCS_GDT     L     117     L     117     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     L     118     L     118     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     E     119     E     119     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     A     120     A     120     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     A     121     A     121     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     V     122     V     122     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     H     123     H     123     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     L     124     L     124     11   14   20     8   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_GDT     Y     125     Y     125     11   14   20     8   11   11   11   13   13   13   14   14   14   14   18   18   18   18   18   20   20   20   20 
LCS_GDT     H     126     H     126     11   14   20     6   11   11   11   13   13   13   14   14   14   16   18   18   18   19   19   20   20   20   20 
LCS_AVERAGE  LCS_A:   7.29  (   4.38    6.48   11.01 )

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      8     11     11     11     13     13     13     14     14     14     16     18     18     18     19     19     20     20     20     20 
GDT PERCENT_CA   5.44   7.48   7.48   7.48   8.84   8.84   8.84   9.52   9.52   9.52  10.88  12.24  12.24  12.24  12.93  12.93  13.61  13.61  13.61  13.61
GDT RMS_LOCAL    0.26   0.51   0.51   0.51   1.37   1.37   1.37   1.92   1.92   1.92   3.98   4.31   4.31   4.31   4.65   4.65   4.94   4.94   4.94   4.94
GDT RMS_ALL_CA  21.57  21.40  21.40  21.40  21.06  21.06  21.06  21.11  21.11  21.11  16.48  16.19  16.19  16.19  17.10  17.10  16.84  16.84  16.84  16.84

#      Molecule1      Molecule2       DISTANCE
LGA    Q      27      Q      27         34.227
LGA    P      28      P      28         33.399
LGA    E      29      E      29         32.893
LGA    D      30      D      30         27.634
LGA    W      31      W      31         23.420
LGA    D      32      D      32         27.447
LGA    K      33      K      33         27.443
LGA    R      34      R      34         29.424
LGA    P      35      P      35         30.959
LGA    I      36      I      36         33.451
LGA    S      37      S      37         38.999
LGA    Y     106      Y     106         30.179
LGA    W     107      W     107         28.950
LGA    G     108      G     108         25.561
LGA    V     109      V     109         23.060
LGA    T     110      T     110         18.380
LGA    D     111      D     111         15.313
LGA    S     112      S     112          9.853
LGA    T     113      T     113          3.927
LGA    T     114      T     114          3.305
LGA    G     115      G     115          2.461
LGA    W     116      W     116          1.379
LGA    L     117      L     117          1.492
LGA    L     118      L     118          1.267
LGA    E     119      E     119          1.405
LGA    A     120      A     120          0.999
LGA    A     121      A     121          0.495
LGA    V     122      V     122          0.873
LGA    H     123      H     123          0.925
LGA    L     124      L     124          1.225
LGA    Y     125      Y     125          2.531
LGA    H     126      H     126          2.661

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32  147    4.0     14    1.92     9.354     8.728     0.693

LGA_LOCAL      RMSD =  1.921  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 21.149  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 13.448  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.815531 * X  +   0.087232 * Y  +   0.572101 * Z  + -48.079338
  Y_new =  -0.190397 * X  +   0.973984 * Y  +   0.122901 * Z  + -12.239631
  Z_new =  -0.546497 * X  +  -0.209156 * Y  +   0.810922 * Z  + -25.985138 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.252422    2.889170  [ DEG:   -14.4627    165.5373 ]
  Theta =   0.578175    2.563417  [ DEG:    33.1270    146.8730 ]
  Phi   =  -0.229356    2.912237  [ DEG:   -13.1411    166.8589 ]
 
# 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: T0369TS464_1_2                                
REMARK     2: T0369.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0369TS464_1_2.T0369.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32  147   4.0   14   1.92   8.728    13.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0369TS464_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0369
PARENT N/A
ATOM      1  CA  GLN    27      12.488  13.161  -0.633  1.00  0.00
ATOM      2  CA  PRO    28      12.715   9.783   1.067  1.00  0.00
ATOM      3  CA  GLU    29       9.488   7.797   1.298  1.00  0.00
ATOM      4  CA  ASP    30       9.091   4.721   3.472  1.00  0.00
ATOM      5  CA  TRP    31       6.912   1.644   2.887  1.00  0.00
ATOM      6  CA  ASP    32       4.150   3.136   5.036  1.00  0.00
ATOM      7  CA  LYS    33       4.153   6.018   2.537  1.00  0.00
ATOM      8  CA  ARG    34       5.574   8.644   4.890  1.00  0.00
ATOM      9  CA  PRO    35       7.784  11.346   3.361  1.00  0.00
ATOM     10  CA  ILE    36      10.910  12.951   4.832  1.00  0.00
ATOM     11  CA  SER    37      12.148  16.036   2.949  1.00  0.00
ATOM     12  CA  TYR   106      12.566  -0.526   1.369  1.00  0.00
ATOM     13  CA  TRP   107      13.745   2.904   0.323  1.00  0.00
ATOM     14  CA  GLY   108      13.180   5.251  -2.621  1.00  0.00
ATOM     15  CA  VAL   109      15.525   8.249  -2.897  1.00  0.00
ATOM     16  CA  THR   110      13.667  10.970  -4.872  1.00  0.00
ATOM     17  CA  ASP   111      15.757  12.998  -7.508  1.00  0.00
ATOM     18  CA  SER   112      14.246  16.363  -8.308  1.00  0.00
ATOM     19  CA  THR   113      10.812  17.641  -7.417  1.00  0.00
ATOM     20  CA  THR   114       8.302  15.902  -9.697  1.00  0.00
ATOM     21  CA  GLY   115       4.710  16.643  -8.688  1.00  0.00
ATOM     22  CA  TRP   116       3.951  12.920  -8.855  1.00  0.00
ATOM     23  CA  LEU   117       6.816  11.545  -6.711  1.00  0.00
ATOM     24  CA  LEU   118       4.906  10.854  -3.487  1.00  0.00
ATOM     25  CA  GLU   119       2.202   9.090  -5.491  1.00  0.00
ATOM     26  CA  ALA   120       4.524   6.774  -7.372  1.00  0.00
ATOM     27  CA  ALA   121       6.787   6.140  -4.392  1.00  0.00
ATOM     28  CA  VAL   122       3.670   5.151  -2.519  1.00  0.00
ATOM     29  CA  HIS   123       2.554   2.905  -5.348  1.00  0.00
ATOM     30  CA  LEU   124       5.910   1.164  -5.730  1.00  0.00
ATOM     31  CA  TYR   125       6.184   0.479  -1.965  1.00  0.00
ATOM     32  CA  HIS   126       2.534  -0.633  -1.664  1.00  0.00
TER
END
