
#######################################################
#                                                     #
#                        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   30 (   30),  selected   30 , name T0331TS464_4_2
# Molecule2: number of CA atoms  139 ( 1101),  selected   30 , name T0331.pdb
# PARAMETERS: T0331TS464_4_2.T0331.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:    17       123 - 139         4.42    19.91
  LCS_AVERAGE:     10.36

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       132 - 139         1.69    18.95
  LCS_AVERAGE:      4.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        82 - 87          0.62    17.86
  LCS_AVERAGE:      3.21

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:  139
LCS_GDT     T      82     T      82      6    7   11     4    6    6    7    7    7    8    9   10   10   10   10   10   10   11   12   13   13   13   14 
LCS_GDT     A      83     A      83      6    7   11     4    6    6    7    7    7    8    9   10   10   10   10   10   10   11   12   13   15   15   17 
LCS_GDT     R      84     R      84      6    7   11     4    6    6    7    7    7    8    9   10   10   10   10   10   11   11   12   13   13   13   17 
LCS_GDT     P      85     P      85      6    7   11     4    6    6    7    7    7    8    9   10   10   10   10   10   11   11   12   13   13   13   14 
LCS_GDT     V      86     V      86      6    7   11     4    6    6    7    7    7    8    9   10   10   10   10   10   11   11   12   13   13   14   15 
LCS_GDT     E      87     E      87      6    7   11     4    6    6    7    7    7    8    9   10   10   10   10   10   11   11   12   13   13   14   15 
LCS_GDT     N      88     N      88      3    7   11     3    3    4    7    7    7    8    9   10   10   10   10   10   11   11   12   13   13   13   14 
LCS_GDT     D      89     D      89      3    4   11     3    3    3    4    5    5    6    9   10   10   10   10   10   11   11   12   13   13   13   14 
LCS_GDT     Y      90     Y      90      3    4   11     3    3    3    4    6    6    8    9   10   10   10   10   10   11   11   12   13   13   13   14 
LCS_GDT     L      91     L      91      3    4   11     3    3    3    4    5    5    6    8   10   10   10   10   10   11   11   12   13   13   13   14 
LCS_GDT     K      92     K      92      3    3   11     3    3    3    3    3    4    5    8    8    9    9   10   10   11   11   12   13   13   13   14 
LCS_GDT     T      93     T      93      3    3   11     3    3    3    3    3    4    5    8    8    9    9   10   10   11   11   12   13   13   13   14 
LCS_GDT     V      94     V      94      3    3   11     3    3    3    3    3    4    6    8    8    9    9   10   10   11   11   12   13   13   13   14 
LCS_GDT     G     123     G     123      4    7   17     3    3    4    5    6    7    8    8   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     F     124     F     124      4    7   17     3    3    4    6    6    7    8    8   11   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     Y     125     Y     125      5    7   17     3    3    5    6    6    7    8    8   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     H     126     H     126      5    7   17     3    4    5    6    6    7    8    8   11   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     S     127     S     127      5    7   17     3    4    5    6    6    7    8    8    9   13   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     L     128     L     128      5    7   17     3    4    5    6    6    7    8    8   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     T     129     T     129      5    7   17     3    4    5    6    6    7    8    8    8   10   15   16   17   17   17   17   17   17   17   17 
LCS_GDT     Q     130     Q     130      3    5   17     3    3    3    4    5    7    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     G     131     G     131      3    6   17     3    3    4    5    6    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     H     132     H     132      5    8   17     4    5    5    6    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     K     133     K     133      5    8   17     4    4    6    7    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     Y     134     Y     134      5    8   17     4    5    6    7    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     I     135     I     135      5    8   17     4    4    6    7    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     F     136     F     136      5    8   17     4    5    6    7    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     S     137     S     137      5    8   17     3    4    6    7    8    9    9   10   11   13   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     I     138     I     138      5    8   17     4    5    6    7    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_GDT     G     139     G     139      3    8   17     4    5    5    7    8    9    9   10   12   14   16   16   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   6.08  (   3.21    4.65   10.36 )

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      4      6      6      7      8      9      9     10     12     14     16     16     17     17     17     17     17     17     17     17 
GDT PERCENT_CA   2.88   4.32   4.32   5.04   5.76   6.47   6.47   7.19   8.63  10.07  11.51  11.51  12.23  12.23  12.23  12.23  12.23  12.23  12.23  12.23
GDT RMS_LOCAL    0.30   0.62   0.62   1.02   1.69   2.03   2.03   2.51   3.62   3.99   4.17   4.17   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42
GDT RMS_ALL_CA  16.71  17.86  17.86  16.72  18.95  17.91  17.91  18.95  19.40  19.71  19.86  19.86  19.91  19.91  19.91  19.91  19.91  19.91  19.91  19.91

#      Molecule1      Molecule2       DISTANCE
LGA    T      82      T      82         26.984
LGA    A      83      A      83         26.323
LGA    R      84      R      84         28.396
LGA    P      85      P      85         28.603
LGA    V      86      V      86         28.483
LGA    E      87      E      87         29.909
LGA    N      88      N      88         27.254
LGA    D      89      D      89         25.669
LGA    Y      90      Y      90         24.331
LGA    L      91      L      91         26.159
LGA    K      92      K      92         31.183
LGA    T      93      T      93         31.501
LGA    V      94      V      94         31.296
LGA    G     123      G     123          5.503
LGA    F     124      F     124          7.124
LGA    Y     125      Y     125          7.064
LGA    H     126      H     126          7.937
LGA    S     127      S     127          8.215
LGA    L     128      L     128          6.568
LGA    T     129      T     129          8.193
LGA    Q     130      Q     130          3.746
LGA    G     131      G     131          2.826
LGA    H     132      H     132          2.974
LGA    K     133      K     133          2.263
LGA    Y     134      Y     134          2.482
LGA    I     135      I     135          2.383
LGA    F     136      F     136          1.974
LGA    S     137      S     137          3.714
LGA    I     138      I     138          1.360
LGA    G     139      G     139          1.589

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30  139    4.0     10    2.51     7.194     6.922     0.383

LGA_LOCAL      RMSD =  2.512  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 18.987  Number of atoms =   30 
Std_ALL_ATOMS  RMSD = 11.928  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.879023 * X  +  -0.379033 * Y  +   0.289226 * Z  +  70.939697
  Y_new =  -0.435474 * X  +   0.885253 * Y  +  -0.163371 * Z  +   0.584041
  Z_new =  -0.194115 * X  +  -0.269557 * Y  +  -0.943217 * Z  +  41.288132 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.863228    0.278365  [ DEG:  -164.0509     15.9491 ]
  Theta =   0.195355    2.946238  [ DEG:    11.1930    168.8070 ]
  Phi   =  -2.681627    0.459966  [ DEG:  -153.6459     26.3541 ]
 
# 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: T0331TS464_4_2                                
REMARK     2: T0331.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0331TS464_4_2.T0331.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30  139   4.0   10   2.51   6.922    11.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0331
PARENT N/A
ATOM      1  CA  THR    82      27.195  32.072   0.046  1.00  0.00
ATOM      2  CA  ALA    83      26.314  34.269   3.020  1.00  0.00
ATOM      3  CA  ARG    84      23.278  36.489   2.895  1.00  0.00
ATOM      4  CA  PRO    85      20.946  38.426   5.140  1.00  0.00
ATOM      5  CA  VAL    86      17.198  37.683   4.955  1.00  0.00
ATOM      6  CA  GLU    87      14.396  40.271   5.139  1.00  0.00
ATOM      7  CA  ASN    88      13.334  38.486   8.377  1.00  0.00
ATOM      8  CA  ASP    89      16.715  39.479   9.944  1.00  0.00
ATOM      9  CA  TYR    90      18.715  36.237   9.827  1.00  0.00
ATOM     10  CA  LEU    91      22.276  35.895   8.578  1.00  0.00
ATOM     11  CA  LYS    92      22.242  32.569   6.635  1.00  0.00
ATOM     12  CA  THR    93      25.907  31.672   6.409  1.00  0.00
ATOM     13  CA  VAL    94      25.323  28.751   4.058  1.00  0.00
ATOM     14  CA  GLY   123      24.559  38.170  20.509  1.00  0.00
ATOM     15  CA  PHE   124      27.061  36.290  18.337  1.00  0.00
ATOM     16  CA  TYR   125      25.583  32.809  18.099  1.00  0.00
ATOM     17  CA  HIS   126      25.923  31.100  14.712  1.00  0.00
ATOM     18  CA  SER   127      23.064  28.742  15.626  1.00  0.00
ATOM     19  CA  LEU   128      23.086  25.241  14.145  1.00  0.00
ATOM     20  CA  THR   129      19.552  24.435  13.038  1.00  0.00
ATOM     21  CA  GLN   130      18.044  20.898  13.036  1.00  0.00
ATOM     22  CA  GLY   131      18.448  20.763   9.260  1.00  0.00
ATOM     23  CA  HIS   132      22.157  21.564   9.280  1.00  0.00
ATOM     24  CA  LYS   133      21.744  25.198   8.296  1.00  0.00
ATOM     25  CA  TYR   134      23.042  28.094  10.423  1.00  0.00
ATOM     26  CA  ILE   135      21.237  31.259  11.556  1.00  0.00
ATOM     27  CA  PHE   136      22.602  34.349  13.309  1.00  0.00
ATOM     28  CA  SER   137      19.949  36.339  15.224  1.00  0.00
ATOM     29  CA  ILE   138      20.775  39.860  16.544  1.00  0.00
ATOM     30  CA  GLY   139      19.342  43.421  16.834  1.00  0.00
TER
END
