
#######################################################
#                                                     #
#                        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   33 (   33),  selected   33 , name T0321TS464_5_2
# Molecule2: number of CA atoms  244 ( 1840),  selected   33 , name T0321.pdb
# PARAMETERS: T0321TS464_5_2.T0321.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:    14       203 - 216         3.10    14.48
  LCS_AVERAGE:      4.71

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       205 - 216         1.68    13.78
  LCS_AVERAGE:      3.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       208 - 216         0.84    14.04
  LCS_AVERAGE:      2.51

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:  244
LCS_GDT     E       3     E       3      5    5    7     5    5    5    5    5    5    5   11   11   16   17   18   18   18   19   19   19   19   19   20 
LCS_GDT     I       4     I       4      5    5    7     5    5    5    5    5    6   10   12   15   16   17   18   18   18   19   19   19   19   19   20 
LCS_GDT     Y       5     Y       5      5    5   10     5    5    5    5    5    5   10   13   15   16   17   18   18   18   19   19   19   19   19   20 
LCS_GDT     D       6     D       6      5    5   10     5    5    5    5    9    9   10   11   15   16   17   18   18   18   19   19   19   19   19   20 
LCS_GDT     A       7     A       7      5    5   10     5    5    5    5    5    5    5    5    6   10   15   16   17   17   19   19   19   19   19   20 
LCS_GDT     V      18     V      18      7    7   10     5    6    7    7    7    7    7    7    7    7    8    8   10   10   11   12   13   14   16   16 
LCS_GDT     D      19     D      19      7    7   10     5    6    7    7    7    7    7    7    7    7    8    8   10   10   11   12   13   14   16   16 
LCS_GDT     E      20     E      20      7    7   10     5    6    7    7    7    7    7    7    7    7    8    8   10   10   11   12   13   14   16   16 
LCS_GDT     L      21     L      21      7    7   10     5    6    7    7    7    7    7    7    7    7    8    8   10   10   11   12   13   16   17   18 
LCS_GDT     V      22     V      22      7    7   10     3    5    7    7    7    7    7    7    7    7    8    8   10   10   11   12   12   12   16   16 
LCS_GDT     C      23     C      23      7    7   10     3    6    7    7    7    7    7    7    7    7    8    8   10   10   11   12   13   14   16   20 
LCS_GDT     G      24     G      24      7    7   10     5    6    7    7    7    7    7    7    7    7    8    8   10   10   11   12   13   14   16   18 
LCS_GDT     N     110     N     110      4    4    7     3    4    4    5    6    6    6    6    8    9   16   16   17   17   18   19   19   19   20   20 
LCS_GDT     D     111     D     111      4    4    7     3    5    8    9   11   12   13   14   15   15   16   16   17   17   18   19   19   19   20   20 
LCS_GDT     P     112     P     112      4    4    8     3    4    4    5    6   11   12   14   15   15   16   16   17   17   18   19   19   19   20   20 
LCS_GDT     F     113     F     113      4    4    8     3    4    4    4    6    6    7   11   13   14   14   16   17   17   18   19   19   19   20   20 
LCS_GDT     I     114     I     114      3    3   13     0    3    3    3    3    3    4    5    6    7   13   15   16   17   18   19   19   19   20   20 
LCS_GDT     M     115     M     115      3    3   13     0    3    3    3    3    3    5    7    8    9   12   15   15   16   17   18   18   18   20   20 
LCS_GDT     S     116     S     116      3    3   13     0    3    3    3    3    3    4    4    5    8   12   12   12   12   14   15   17   17   18   19 
LCS_GDT     T     203     T     203      3    3   14     0    3    3    3    5    5    7    8   10   15   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     P     204     P     204      3    4   14     3    3    4    4    5    7   11   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     L     205     L     205      3   12   14     3    6    6    8   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     A     206     A     206      5   12   14     3    4    5    9   11   11   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     P     207     P     207      8   12   14     3    6    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     V     208     V     208      9   12   14     6    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     L     209     L     209      9   12   14     6    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     F     210     F     210      9   12   14     6    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     E     211     E     211      9   12   14     6    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     H     212     H     212      9   12   14     6    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     G     213     G     213      9   12   14     6    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     L     214     L     214      9   12   14     3    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     Q     215     Q     215      9   12   14     3    8    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_GDT     E     216     E     216      9   12   14     3    6    9   10   11   12   13   14   15   16   17   18   18   18   19   19   19   19   20   20 
LCS_AVERAGE  LCS_A:   3.44  (   2.51    3.10    4.71 )

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      6      8      9     10     11     12     13     14     15     16     17     18     18     18     19     19     19     19     20     20 
GDT PERCENT_CA   2.46   3.28   3.69   4.10   4.51   4.92   5.33   5.74   6.15   6.56   6.97   7.38   7.38   7.38   7.79   7.79   7.79   7.79   8.20   8.20
GDT RMS_LOCAL    0.26   0.69   0.84   1.07   1.41   1.75   2.04   2.43   2.85   3.36   3.54   3.77   3.77   3.77   4.12   4.12   4.12   4.12   5.48   4.74
GDT RMS_ALL_CA  14.16  14.18  14.04  13.84  13.76  14.44  14.24  14.56  14.43  14.88  14.84  15.38  15.38  15.38  15.50  15.50  15.50  15.50  15.23  15.56

#      Molecule1      Molecule2       DISTANCE
LGA    E       3      E       3         16.125
LGA    I       4      I       4         12.375
LGA    Y       5      Y       5          9.580
LGA    D       6      D       6         13.471
LGA    A       7      A       7         16.573
LGA    V      18      V      18         32.582
LGA    D      19      D      19         32.931
LGA    E      20      E      20         28.200
LGA    L      21      L      21         24.732
LGA    V      22      V      22         21.457
LGA    C      23      C      23         21.224
LGA    G      24      G      24         19.088
LGA    N     110      N     110          7.842
LGA    D     111      D     111          2.380
LGA    P     112      P     112          3.709
LGA    F     113      F     113          8.192
LGA    I     114      I     114         13.086
LGA    M     115      M     115         16.096
LGA    S     116      S     116         21.755
LGA    T     203      T     203         11.448
LGA    P     204      P     204          6.241
LGA    L     205      L     205          1.610
LGA    A     206      A     206          3.787
LGA    P     207      P     207          1.671
LGA    V     208      V     208          3.829
LGA    L     209      L     209          2.405
LGA    F     210      F     210          0.895
LGA    E     211      E     211          3.095
LGA    H     212      H     212          1.732
LGA    G     213      G     213          1.150
LGA    L     214      L     214          1.021
LGA    Q     215      Q     215          1.632
LGA    E     216      E     216          3.120

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  244    4.0     14    2.43     5.225     4.855     0.554

LGA_LOCAL      RMSD =  2.426  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.647  Number of atoms =   33 
Std_ALL_ATOMS  RMSD = 12.840  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.088566 * X  +   0.870283 * Y  +   0.484524 * Z  + -48.788620
  Y_new =  -0.847872 * X  +   0.189420 * Y  +  -0.495210 * Z  + 127.464798
  Z_new =  -0.522752 * X  +  -0.454673 * Y  +   0.721112 * Z  +  94.700317 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.562556    2.579036  [ DEG:   -32.2321    147.7679 ]
  Theta =   0.550076    2.591517  [ DEG:    31.5170    148.4830 ]
  Phi   =  -1.674876    1.466717  [ DEG:   -95.9633     84.0367 ]
 
# 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: T0321TS464_5_2                                
REMARK     2: T0321.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_5_2.T0321.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  244   4.0   14   2.43   4.855    12.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3       2.969  47.429  64.040  1.00  0.00
ATOM      2  CA  ILE     4       3.230  45.136  67.076  1.00  0.00
ATOM      3  CA  TYR     5       1.525  42.102  65.508  1.00  0.00
ATOM      4  CA  ASP     6       3.070  42.808  62.087  1.00  0.00
ATOM      5  CA  ALA     7       6.505  43.377  63.529  1.00  0.00
ATOM      6  CA  VAL    18       9.952  39.667  78.261  1.00  0.00
ATOM      7  CA  ASP    19      11.041  41.517  75.108  1.00  0.00
ATOM      8  CA  GLU    20       8.492  44.301  74.747  1.00  0.00
ATOM      9  CA  LEU    21       5.495  45.771  76.456  1.00  0.00
ATOM     10  CA  VAL    22       2.279  46.986  75.022  1.00  0.00
ATOM     11  CA  CYS    23       0.661  49.490  77.372  1.00  0.00
ATOM     12  CA  GLY    24      -2.672  50.731  76.062  1.00  0.00
ATOM     13  CA  ASN   110      15.804  48.018  78.064  1.00  0.00
ATOM     14  CA  ASP   111      12.459  46.605  76.893  1.00  0.00
ATOM     15  CA  PRO   112      10.763  47.661  73.651  1.00  0.00
ATOM     16  CA  PHE   113       7.692  49.741  74.501  1.00  0.00
ATOM     17  CA  ILE   114       4.448  50.183  72.534  1.00  0.00
ATOM     18  CA  MET   115       1.752  52.622  73.598  1.00  0.00
ATOM     19  CA  SER   116      -1.770  53.433  72.437  1.00  0.00
ATOM     20  CA  THR   203      -6.020  41.927  76.479  1.00  0.00
ATOM     21  CA  PRO   204      -7.087  42.587  72.899  1.00  0.00
ATOM     22  CA  LEU   205      -3.365  42.748  71.936  1.00  0.00
ATOM     23  CA  ALA   206      -2.640  39.313  73.423  1.00  0.00
ATOM     24  CA  PRO   207      -5.626  37.792  71.684  1.00  0.00
ATOM     25  CA  VAL   208      -4.174  39.386  68.546  1.00  0.00
ATOM     26  CA  LEU   209      -0.679  38.132  68.833  1.00  0.00
ATOM     27  CA  PHE   210      -1.835  34.617  69.831  1.00  0.00
ATOM     28  CA  GLU   211      -4.054  34.483  66.761  1.00  0.00
ATOM     29  CA  HIS   212      -0.889  35.006  64.757  1.00  0.00
ATOM     30  CA  GLY   213       1.504  32.366  66.027  1.00  0.00
ATOM     31  CA  LEU   214       3.333  34.725  68.378  1.00  0.00
ATOM     32  CA  GLN   215       3.899  33.349  71.885  1.00  0.00
ATOM     33  CA  GLU   216       2.879  36.158  74.213  1.00  0.00
TER
END
