
#######################################################
#                                                     #
#                        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   23 (   23),  selected   23 , name T0321TS464_2_2-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected   23 , name T0321_D2.pdb
# PARAMETERS: T0321TS464_2_2-D2.T0321_D2.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       203 - 218         3.63     9.25
  LCS_AVERAGE:      9.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       206 - 216         1.81     9.00
  LCS_AVERAGE:      5.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       206 - 213         0.84    13.53
  LCS_AVERAGE:      3.47

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:  148
LCS_GDT     N     110     N     110      4    4    7     3    4    4    4    6   11   11   12   13   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     D     111     D     111      4    4    7     3    7    7    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     P     112     P     112      4    4    8     3    4    6    7   10   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     F     113     F     113      4    4    8     3    4    5    8    9    9   10   11   12   14   16   16   18   20   20   20   21   21   21   22 
LCS_GDT     I     114     I     114      3    3   13     0    3    3    3    3    3    4    9   11   11   14   16   17   17   19   20   21   21   21   22 
LCS_GDT     M     115     M     115      3    3   14     0    3    3    3    3    4    7    7    8   11   13   14   16   17   18   18   18   19   21   22 
LCS_GDT     S     116     S     116      3    3   14     0    3    3    3    3    3    4    4    5    8   11   12   13   14   15   16   17   19   19   19 
LCS_GDT     T     203     T     203      3    3   16     0    3    3    3    3    5    8   10   12   14   16   16   18   20   20   20   21   21   21   22 
LCS_GDT     P     204     P     204      3    4   16     3    3    3    3    5    8   11   13   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     L     205     L     205      3   10   16     3    3    3    7   10   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     A     206     A     206      8   11   16     3    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     P     207     P     207      8   11   16     3    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     V     208     V     208      8   11   16     3    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     L     209     L     209      8   11   16     4    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     F     210     F     210      8   11   16     4    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     E     211     E     211      8   11   16     4    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     H     212     H     212      8   11   16     4    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     G     213     G     213      8   11   16     4    7    8    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     L     214     L     214      4   11   16     3    7    7    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     Q     215     Q     215      4   11   16     4    7    7    8   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     E     216     E     216      4   11   16     4    7    7    9   12   14   14   14   15   15   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     L     217     L     217      4    7   16     4    4    4    8    9    9   13   13   13   13   16   17   18   20   20   20   21   21   21   22 
LCS_GDT     S     218     S     218      4    7   16     4    7    8    9   10   11   13   13   14   14   16   17   18   20   20   20   21   21   21   22 
LCS_AVERAGE  LCS_A:   6.09  (   3.47    5.20    9.61 )

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      7      8      9     12     14     14     14     15     15     16     17     18     20     20     20     21     21     21     22 
GDT PERCENT_CA   2.70   4.73   5.41   6.08   8.11   9.46   9.46   9.46  10.14  10.14  10.81  11.49  12.16  13.51  13.51  13.51  14.19  14.19  14.19  14.86
GDT RMS_LOCAL    0.30   0.51   0.77   0.95   1.78   2.17   2.17   2.17   2.70   2.54   3.10   3.36   3.65   4.30   4.30   4.30   4.88   4.88   4.88   5.61
GDT RMS_ALL_CA  14.49  11.91  11.82  11.97   8.53   7.87   7.87   7.87   7.51   8.16   7.14   8.41   8.02   7.30   7.30   7.30   6.90   6.90   6.90   6.60

#      Molecule1      Molecule2       DISTANCE
LGA    N     110      N     110          6.372
LGA    D     111      D     111          1.699
LGA    P     112      P     112          3.075
LGA    F     113      F     113          8.740
LGA    I     114      I     114         13.437
LGA    M     115      M     115         16.532
LGA    S     116      S     116         22.108
LGA    T     203      T     203         11.480
LGA    P     204      P     204          7.531
LGA    L     205      L     205          3.017
LGA    A     206      A     206          2.764
LGA    P     207      P     207          2.076
LGA    V     208      V     208          2.576
LGA    L     209      L     209          2.038
LGA    F     210      F     210          1.820
LGA    E     211      E     211          2.080
LGA    H     212      H     212          1.100
LGA    G     213      G     213          2.261
LGA    L     214      L     214          0.273
LGA    Q     215      Q     215          2.294
LGA    E     216      E     216          1.529
LGA    L     217      L     217          7.407
LGA    S     218      S     218          7.572

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  148    4.0     14    2.17     8.446     8.054     0.617

LGA_LOCAL      RMSD =  2.168  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.874  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  6.459  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.225761 * X  +  -0.388120 * Y  +  -0.893529 * Z  +  51.112297
  Y_new =  -0.967781 * X  +   0.015624 * Y  +  -0.251308 * Z  + 105.248566
  Z_new =   0.111499 * X  +   0.921476 * Y  +  -0.372088 * Z  +  63.467957 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.954571   -1.187022  [ DEG:   111.9886    -68.0114 ]
  Theta =  -0.111731   -3.029862  [ DEG:    -6.4017   -173.5983 ]
  Phi   =  -1.341618    1.799975  [ DEG:   -76.8690    103.1310 ]
 
# 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_2_2-D2                             
REMARK     2: T0321_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_2_2-D2.T0321_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  148   4.0   14   2.17   8.054     6.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM     22  CA  ASN   110      14.615  48.073  79.337  1.00  0.00
ATOM     23  CA  ASP   111      11.368  46.570  78.013  1.00  0.00
ATOM     24  CA  PRO   112       9.977  47.320  74.549  1.00  0.00
ATOM     25  CA  PHE   113       6.871  49.485  74.922  1.00  0.00
ATOM     26  CA  ILE   114       3.818  49.753  72.643  1.00  0.00
ATOM     27  CA  MET   115       1.071  52.295  73.228  1.00  0.00
ATOM     28  CA  SER   116      -2.324  53.008  71.688  1.00  0.00
ATOM     29  CA  THR   203      -6.512  42.167  76.246  1.00  0.00
ATOM     30  CA  PRO   204      -8.446  41.989  72.986  1.00  0.00
ATOM     31  CA  LEU   205      -5.141  42.625  71.120  1.00  0.00
ATOM     32  CA  ALA   206      -3.403  39.686  72.814  1.00  0.00
ATOM     33  CA  PRO   207      -6.305  37.384  72.082  1.00  0.00
ATOM     34  CA  VAL   208      -4.925  38.309  68.640  1.00  0.00
ATOM     35  CA  LEU   209      -1.405  37.178  69.615  1.00  0.00
ATOM     36  CA  PHE   210      -2.726  33.761  70.625  1.00  0.00
ATOM     37  CA  GLU   211      -4.371  33.237  67.203  1.00  0.00
ATOM     38  CA  HIS   212      -1.323  34.478  65.286  1.00  0.00
ATOM     39  CA  GLY   213       1.169  32.298  67.194  1.00  0.00
ATOM     40  CA  LEU   214       3.101  35.459  68.107  1.00  0.00
ATOM     41  CA  GLN   215       6.183  34.809  70.249  1.00  0.00
ATOM     42  CA  GLU   216       5.577  37.385  72.982  1.00  0.00
ATOM     43  CA  LEU   217       7.257  37.462  76.384  1.00  0.00
ATOM     44  CA  SER   218       4.968  39.454  78.659  1.00  0.00
TER
END
