
#######################################################
#                                                     #
#                        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   10 (   84),  selected   10 , name T0386TS074_2_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   10 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_2_2-D1.T0386_D1.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:    10       209 - 218         0.85     0.85
  LCS_AVERAGE:      4.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.85     0.85
  LCS_AVERAGE:      4.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.85     0.85
  LCS_AVERAGE:      4.85

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:  206
LCS_GDT     P     209     P     209     10   10   10     3    6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     M     210     M     210     10   10   10     3    6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     Q     211     Q     211     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     H     212     H     212     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     213     L     213     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     F     214     F     214     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E     215     E     215     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     216     D     216     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     I     217     I     217     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     S     218     S     218     10   10   10     5    8   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   4.85  (   4.85    4.85    4.85 )

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      5      8     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.43   3.88   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85
GDT RMS_LOCAL    0.18   0.51   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85
GDT RMS_ALL_CA   1.30   0.99   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209          1.409
LGA    M     210      M     210          1.355
LGA    Q     211      Q     211          0.592
LGA    H     212      H     212          0.720
LGA    L     213      L     213          0.437
LGA    F     214      F     214          0.288
LGA    E     215      E     215          0.764
LGA    D     216      D     216          0.881
LGA    I     217      I     217          0.669
LGA    S     218      S     218          0.614

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  206    4.0     10    0.85     4.612     4.778     1.058

LGA_LOCAL      RMSD =  0.845  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.845  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  0.845  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.332602 * X  +  -0.873560 * Y  +  -0.355344 * Z  +  60.350899
  Y_new =  -0.929867 * X  +  -0.240953 * Y  +  -0.278010 * Z  +  62.181084
  Z_new =   0.157237 * X  +   0.422889 * Y  +  -0.892436 * Z  +  42.392071 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.699075   -0.442518  [ DEG:   154.6456    -25.3544 ]
  Theta =  -0.157892   -2.983701  [ DEG:    -9.0465   -170.9535 ]
  Phi   =  -1.227289    1.914304  [ DEG:   -70.3185    109.6815 ]
 
# 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: T0386TS074_2_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_2_2-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  206   4.0   10   0.85   4.778     0.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      16.055  49.400  68.690  1.00  0.92
ATOM   1387  CA  PRO   209      15.830  50.580  67.869  1.00  0.92
ATOM   1388  C   PRO   209      14.377  50.517  67.493  1.00  0.92
ATOM   1389  O   PRO   209      13.626  51.403  67.881  1.00  0.92
ATOM   1390  CB  PRO   209      16.616  50.587  66.545  1.00  0.92
ATOM   1391  CG  PRO   209      17.500  49.361  66.309  1.00  1.02
ATOM   1392  CD  PRO   209      16.559  48.315  67.387  1.00  1.02
ATOM   1393  N   MET   210      14.014  49.420  66.808  1.00  0.80
ATOM   1394  CA  MET   210      12.694  49.236  66.267  1.00  0.80
ATOM   1395  C   MET   210      11.560  49.455  67.231  1.00  0.80
ATOM   1396  O   MET   210      10.727  50.306  66.960  1.00  0.80
ATOM   1397  CB  MET   210      12.601  47.839  65.653  1.00  0.80
ATOM   1398  CG  MET   210      11.270  47.517  64.968  1.00  0.90
ATOM   1399  SD  MET   210      10.971  48.572  63.493  1.00  0.90
ATOM   1400  CE  MET   210       9.408  47.967  62.955  1.00  1.10
ATOM   1401  N   GLN   211      11.597  49.085  68.329  1.00  0.80
ATOM   1402  CA  GLN   211      10.422  49.011  69.201  1.00  0.80
ATOM   1403  C   GLN   211      10.371  50.133  70.260  1.00  0.80
ATOM   1404  O   GLN   211       9.310  50.699  70.504  1.00  0.80
ATOM   1405  CB  GLN   211      10.303  47.621  69.849  1.00  0.80
ATOM   1406  CG  GLN   211       9.086  47.426  70.710  1.00  0.90
ATOM   1407  CD  GLN   211       7.801  47.471  70.021  1.00  0.90
ATOM   1408  OE1 GLN   211       7.568  46.648  69.117  1.00  1.10
ATOM   1409  NE2 GLN   211       6.899  48.368  70.410  1.00  1.10
ATOM   1410  N   HIS   212      11.507  50.468  70.861  1.00  0.80
ATOM   1411  CA  HIS   212      11.539  51.473  71.910  1.00  0.80
ATOM   1412  C   HIS   212      11.261  52.883  71.372  1.00  0.80
ATOM   1413  O   HIS   212      10.502  53.660  71.976  1.00  0.80
ATOM   1414  CB  HIS   212      12.874  51.431  72.641  1.00  0.80
ATOM   1415  CG  HIS   212      12.989  52.405  73.819  1.00  0.90
ATOM   1416  ND1 HIS   212      13.273  53.765  73.604  1.00  0.90
ATOM   1417  CD2 HIS   212      12.753  52.183  75.099  1.00  1.10
ATOM   1418  CE1 HIS   212      13.235  54.401  74.821  1.00  1.10
ATOM   1419  NE2 HIS   212      12.917  53.424  75.760  1.00  1.40
ATOM   1420  N   LEU   213      11.863  53.212  70.229  1.00  0.80
ATOM   1421  CA  LEU   213      11.617  54.483  69.558  1.00  0.80
ATOM   1422  C   LEU   213      10.161  54.574  69.127  1.00  0.80
ATOM   1423  O   LEU   213       9.522  55.607  69.335  1.00  0.80
ATOM   1424  CB  LEU   213      12.590  54.693  68.360  1.00  0.80
ATOM   1425  CG  LEU   213      12.336  56.068  67.744  1.00  0.90
ATOM   1426  CD1 LEU   213      12.670  57.137  68.685  1.00  0.90
ATOM   1427  CD2 LEU   213      13.507  56.226  66.588  1.00  1.10
ATOM   1428  N   PHE   214       9.622  53.509  68.536  1.00  0.80
ATOM   1429  CA  PHE   214       8.216  53.528  68.123  1.00  0.80
ATOM   1430  C   PHE   214       7.283  53.716  69.352  1.00  0.80
ATOM   1431  O   PHE   214       6.516  54.671  69.422  1.00  0.80
ATOM   1432  CB  PHE   214       7.825  52.258  67.322  1.00  0.80
ATOM   1433  CG  PHE   214       8.593  52.206  65.991  1.00  0.90
ATOM   1434  CD1 PHE   214       8.946  53.429  65.402  1.00  0.90
ATOM   1435  CD2 PHE   214       8.503  51.092  65.189  1.00  1.10
ATOM   1436  CE1 PHE   214       9.409  53.434  64.102  1.00  1.10
ATOM   1437  CE2 PHE   214       8.976  51.062  63.903  1.00  1.40
ATOM   1438  CZ  PHE   214       9.465  52.276  63.350  1.00  1.40
ATOM   1439  N   GLU   215       7.386  52.843  70.338  1.00  0.80
ATOM   1440  CA  GLU   215       6.437  52.870  71.443  1.00  0.80
ATOM   1441  C   GLU   215       6.583  54.022  72.454  1.00  0.80
ATOM   1442  O   GLU   215       5.575  54.560  72.884  1.00  0.80
ATOM   1443  CB  GLU   215       6.316  51.481  72.091  1.00  0.80
ATOM   1444  CG  GLU   215       5.289  51.456  73.190  1.00  0.90
ATOM   1445  CD  GLU   215       3.842  51.713  72.659  1.00  0.90
ATOM   1446  OE1 GLU   215       3.591  51.728  71.445  1.00  1.10
ATOM   1447  OE2 GLU   215       2.955  51.948  73.525  1.00  1.10
ATOM   1448  N   ASP   216       7.810  54.397  72.816  1.00  0.80
ATOM   1449  CA  ASP   216       8.027  55.580  73.649  1.00  0.80
ATOM   1450  C   ASP   216       7.633  56.842  72.892  1.00  0.80
ATOM   1451  O   ASP   216       7.204  57.824  73.504  1.00  0.80
ATOM   1452  CB  ASP   216       9.470  55.683  74.141  1.00  0.80
ATOM   1453  CG  ASP   216       9.847  54.640  75.165  1.00  0.90
ATOM   1454  OD1 ASP   216       8.973  53.962  75.761  1.00  0.90
ATOM   1455  OD2 ASP   216      11.019  54.480  75.517  1.00  1.10
ATOM   1456  N   ILE   217       7.770  56.807  71.564  1.00  0.80
ATOM   1457  CA  ILE   217       7.355  57.891  70.696  1.00  0.80
ATOM   1458  C   ILE   217       5.852  58.083  70.649  1.00  0.80
ATOM   1459  O   ILE   217       5.369  59.206  70.724  1.00  0.80
ATOM   1460  CB  ILE   217       7.195  58.740  71.959  1.00  0.80
ATOM   1461  CG1 ILE   217       6.654  60.152  71.724  1.00  0.90
ATOM   1462  CG2 ILE   217       8.538  58.718  72.699  1.00  0.90
ATOM   1463  CD1 ILE   217       6.169  60.850  72.955  1.00  1.10
ATOM   1464  N   SER   218       5.108  56.993  70.475  1.00  0.80
ATOM   1465  CA  SER   218       3.649  57.000  70.555  1.00  0.80
ATOM   1466  C   SER   218       3.184  57.539  71.913  1.00  0.80
ATOM   1467  O   SER   218       2.281  58.361  71.974  1.00  0.80
ATOM   1468  CB  SER   218       3.059  55.574  70.331  1.00  0.80
ATOM   1469  OG  SER   218       3.537  54.606  71.413  1.00  0.90
TER
END
