
#######################################################
#                                                     #
#                        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 T0328TS464_2_2
# Molecule2: number of CA atoms  307 ( 2453),  selected   30 , name T0328.pdb
# PARAMETERS: T0328TS464_2_2.T0328.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:    12       170 - 181         4.79    19.38
  LCS_AVERAGE:      3.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       176 - 182         1.39    22.97
  LCS_AVERAGE:      1.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       177 - 182         0.86    23.17
  LCS_AVERAGE:      1.42

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:  307
LCS_GDT     G      17     G      17      4    4   10     3    5    5    6    6    6    8    9   10   11   12   12   12   14   14   14   14   14   15   15 
LCS_GDT     N      18     N      18      4    4   10     3    3    4    4    4    7    8    9   10   11   12   12   12   14   14   14   14   14   15   15 
LCS_GDT     L      19     L      19      4    4   10     3    3    4    4    4    4    5    6    8   10   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     H      20     H      20      4    4   10     3    3    4    4    4    4    5    7   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     S      21     S      21      3    4   10     3    3    3    3    4    4    5    7   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     A      95     A      95      5    5   10     4    5    6    6    6    6    8    9   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     P      96     P      96      5    5   10     4    5    6    6    6    6    8    9   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     A      97     A      97      5    5   10     4    5    6    6    6    6    8    9   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     I      98     I      98      5    5   10     4    4    6    6    6    6    8    9   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     E      99     E      99      5    5   10     3    5    6    6    6    6    8    9   10   11   12   12   12   13   13   13   14   14   14   15 
LCS_GDT     L     146     L     146      3    5    7     3    3    3    4    4    4    7    7    7    8    8    9    9   10   10   10   10   10   12   13 
LCS_GDT     T     147     T     147      3    5    7     3    3    3    4    4    6    7    7    7    8    8    9    9   10   10   10   10   10   12   13 
LCS_GDT     G     148     G     148      4    5    7     4    4    4    5    5    6    7    7    7    8    8    9    9   10   10   10   10   10   12   13 
LCS_GDT     F     149     F     149      4    5    7     4    4    4    5    5    6    7    7    7    8    8    9    9   10   10   10   10   10   11   13 
LCS_GDT     V     150     V     150      4    5    7     4    4    4    5    5    6    7    7    7    8    8    9    9   10   10   10   10   10   10   12 
LCS_GDT     D     151     D     151      4    5    7     4    4    4    5    5    6    7    7    7    8    8    9    9   10   10   10   14   14   14   15 
LCS_GDT     G     152     G     152      4    5    7     0    3    4    5    5    6    7    7    7    8    8    9    9   10   10   10   10   11   11   14 
LCS_GDT     E     170     E     170      4    4   12     3    4    4    4    4    5    5    7    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     D     171     D     171      4    4   12     3    4    4    4    4    5    5    7    8   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     P     172     P     172      4    4   12     3    4    4    4    4    5    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     E     173     E     173      4    5   12     3    4    4    5    5    6    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     F     174     F     174      3    5   12     3    3    3    5    5    6    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     K     175     K     175      3    5   12     3    3    3    5    5    6    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     G     176     G     176      3    7   12     3    3    3    5    7    7    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     G     177     G     177      6    7   12     3    5    6    6    7    7    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     S     178     S     178      6    7   12     3    5    6    6    7    7    7    8    9   10   10   11   11   14   14   14   14   14   15   15 
LCS_GDT     Y     179     Y     179      6    7   12     3    5    6    6    7    7    7    9   10   11   12   12   12   14   14   14   14   14   15   15 
LCS_GDT     I     180     I     180      6    7   12     3    5    6    6    7    7    8    9   10   11   12   12   12   14   14   14   14   14   15   15 
LCS_GDT     H     181     H     181      6    7   12     3    5    6    6    7    7    7    7    8    8    9   10   12   14   14   14   14   14   15   15 
LCS_GDT     V     182     V     182      6    7   10     3    4    6    6    7    7    7    7    7    7    9    9   10   10   11   11   11   11   15   15 
LCS_AVERAGE  LCS_A:   2.14  (   1.42    1.69    3.29 )

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      5      6      6      7      7      8      9     10     11     12     12     12     14     14     14     14     14     15     15 
GDT PERCENT_CA   1.30   1.63   1.95   1.95   2.28   2.28   2.61   2.93   3.26   3.58   3.91   3.91   3.91   4.56   4.56   4.56   4.56   4.56   4.89   4.89
GDT RMS_LOCAL    0.36   0.56   0.86   0.86   1.39   1.39   2.30   2.63   3.17   3.48   3.79   3.79   3.79   5.60   5.60   5.60   5.10   5.10   6.24   5.72
GDT RMS_ALL_CA  16.23  15.73  23.17  23.17  22.97  22.97  15.36  15.37  15.25  15.16  15.02  15.02  15.02  18.14  18.14  18.14  14.92  14.92  17.96  15.08

#      Molecule1      Molecule2       DISTANCE
LGA    G      17      G      17          2.592
LGA    N      18      N      18          2.996
LGA    L      19      L      19          6.651
LGA    H      20      H      20          5.444
LGA    S      21      S      21          5.182
LGA    A      95      A      95          2.447
LGA    P      96      P      96          2.816
LGA    A      97      A      97          1.891
LGA    I      98      I      98          3.489
LGA    E      99      E      99          2.582
LGA    L     146      L     146         22.070
LGA    T     147      T     147         23.830
LGA    G     148      G     148         21.324
LGA    F     149      F     149         19.049
LGA    V     150      V     150         17.280
LGA    D     151      D     151         11.966
LGA    G     152      G     152         15.284
LGA    E     170      E     170         27.336
LGA    D     171      D     171         22.586
LGA    P     172      P     172         22.534
LGA    E     173      E     173         21.243
LGA    F     174      F     174         17.889
LGA    K     175      K     175         21.213
LGA    G     176      G     176         22.763
LGA    G     177      G     177         17.708
LGA    S     178      S     178         10.448
LGA    Y     179      Y     179          3.912
LGA    I     180      I     180          3.024
LGA    H     181      H     181          8.958
LGA    V     182      V     182         12.821

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30  307    4.0      9    2.63     2.769     2.575     0.330

LGA_LOCAL      RMSD =  2.627  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.163  Number of atoms =   30 
Std_ALL_ATOMS  RMSD = 12.890  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.413150 * X  +   0.185465 * Y  +   0.891577 * Z  + -15.632849
  Y_new =   0.449904 * X  +  -0.809648 * Y  +   0.376904 * Z  +  77.672493
  Z_new =   0.791766 * X  +   0.556842 * Y  +   0.251064 * Z  + -10.634399 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.147218   -1.994375  [ DEG:    65.7307   -114.2693 ]
  Theta =  -0.913695   -2.227897  [ DEG:   -52.3509   -127.6491 ]
  Phi   =   2.313634   -0.827959  [ DEG:   132.5615    -47.4385 ]
 
# 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: T0328TS464_2_2                                
REMARK     2: T0328.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0328TS464_2_2.T0328.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30  307   4.0    9   2.63   2.575    12.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0328TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0328
PARENT N/A
ATOM      1  CA  GLY    17      17.759  19.043  45.356  1.00  0.00
ATOM      2  CA  ASN    18      20.100  22.033  45.627  1.00  0.00
ATOM      3  CA  LEU    19      23.873  22.347  45.196  1.00  0.00
ATOM      4  CA  HIS    20      26.363  24.464  47.095  1.00  0.00
ATOM      5  CA  SER    21      29.893  25.403  45.957  1.00  0.00
ATOM      6  CA  ALA    95      29.234  39.514  36.555  1.00  0.00
ATOM      7  CA  PRO    96      32.731  39.034  37.935  1.00  0.00
ATOM      8  CA  ALA    97      35.747  36.906  37.104  1.00  0.00
ATOM      9  CA  ILE    98      36.086  34.191  39.814  1.00  0.00
ATOM     10  CA  GLU    99      39.373  32.398  40.411  1.00  0.00
ATOM     11  CA  LEU   146      29.092  19.541  38.792  1.00  0.00
ATOM     12  CA  THR   147      29.389  21.864  35.795  1.00  0.00
ATOM     13  CA  GLY   148      27.310  24.824  37.017  1.00  0.00
ATOM     14  CA  PHE   149      27.418  28.324  35.545  1.00  0.00
ATOM     15  CA  VAL   150      28.248  31.201  37.848  1.00  0.00
ATOM     16  CA  ASP   151      25.905  34.076  38.564  1.00  0.00
ATOM     17  CA  GLY   152      28.391  35.696  40.900  1.00  0.00
ATOM     18  CA  GLU   170      42.897  25.859  42.443  1.00  0.00
ATOM     19  CA  ASP   171      44.100  27.320  39.113  1.00  0.00
ATOM     20  CA  PRO   172      40.578  28.228  38.071  1.00  0.00
ATOM     21  CA  GLU   173      39.624  31.382  36.127  1.00  0.00
ATOM     22  CA  PHE   174      35.907  31.643  35.295  1.00  0.00
ATOM     23  CA  LYS   175      34.705  34.585  33.169  1.00  0.00
ATOM     24  CA  GLY   176      31.575  36.502  34.067  1.00  0.00
ATOM     25  CA  GLY   177      28.350  34.491  33.420  1.00  0.00
ATOM     26  CA  SER   178      30.033  31.344  32.126  1.00  0.00
ATOM     27  CA  TYR   179      31.020  27.736  32.865  1.00  0.00
ATOM     28  CA  ILE   180      34.147  25.535  32.761  1.00  0.00
ATOM     29  CA  HIS   181      34.660  21.800  33.324  1.00  0.00
ATOM     30  CA  VAL   182      37.444  20.602  35.634  1.00  0.00
TER
END
