
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   10 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_1_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         0.90     0.90
  LCS_AVERAGE:      4.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.90     0.90
  LCS_AVERAGE:      4.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.90     0.90
  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    5   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    5   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    7   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    7   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    7   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    7   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    7   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     4    7   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     4    7   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     0    3   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      7     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.43   3.40   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   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90
GDT RMS_ALL_CA   1.32   1.08   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209          1.335
LGA    M     210      M     210          1.422
LGA    Q     211      Q     211          0.575
LGA    H     212      H     212          0.632
LGA    L     213      L     213          0.400
LGA    F     214      F     214          0.446
LGA    E     215      E     215          0.734
LGA    D     216      D     216          0.823
LGA    I     217      I     217          0.817
LGA    S     218      S     218          1.184

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  206    4.0     10    0.90     4.490     4.739     0.996

LGA_LOCAL      RMSD =  0.904  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.904  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  0.904  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.250394 * X  +  -0.938797 * Y  +  -0.236565 * Z  +  63.690792
  Y_new =  -0.944080 * X  +  -0.182628 * Y  +  -0.274517 * Z  +  58.714901
  Z_new =   0.214513 * X  +   0.292074 * Y  +  -0.932029 * Z  +  50.588818 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.837912   -0.303681  [ DEG:   162.6004    -17.3996 ]
  Theta =  -0.216193   -2.925400  [ DEG:   -12.3869   -167.6131 ]
  Phi   =  -1.311540    1.830053  [ DEG:   -75.1457    104.8543 ]
 
# 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_1_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_1_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   0.90   4.739     0.90
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      16.159  49.283  68.724  1.00  1.05
ATOM   1387  CA  PRO   209      15.958  50.468  67.904  1.00  1.05
ATOM   1388  C   PRO   209      14.511  50.424  67.509  1.00  1.05
ATOM   1389  O   PRO   209      13.764  51.317  67.889  1.00  1.05
ATOM   1390  CB  PRO   209      16.762  50.469  66.591  1.00  1.05
ATOM   1391  CG  PRO   209      17.634  49.233  66.363  1.00  1.15
ATOM   1392  CD  PRO   209      16.667  48.196  67.426  1.00  1.15
ATOM   1393  N   MET   210      14.142  49.332  66.816  1.00  0.90
ATOM   1394  CA  MET   210      12.828  49.165  66.257  1.00  0.90
ATOM   1395  C   MET   210      11.686  49.396  67.207  1.00  0.90
ATOM   1396  O   MET   210      10.865  50.256  66.927  1.00  0.90
ATOM   1397  CB  MET   210      12.727  47.770  65.639  1.00  0.90
ATOM   1398  CG  MET   210      11.401  47.466  64.936  1.00  1.00
ATOM   1399  SD  MET   210      11.135  48.528  63.460  1.00  1.00
ATOM   1400  CE  MET   210       9.571  47.943  62.899  1.00  1.20
ATOM   1401  N   GLN   211      11.702  49.023  68.306  1.00  0.90
ATOM   1402  CA  GLN   211      10.516  48.961  69.161  1.00  0.90
ATOM   1403  C   GLN   211      10.463  50.081  70.222  1.00  0.90
ATOM   1404  O   GLN   211       9.407  50.659  70.454  1.00  0.90
ATOM   1405  CB  GLN   211      10.371  47.572  69.805  1.00  0.90
ATOM   1406  CG  GLN   211       9.141  47.388  70.648  1.00  1.00
ATOM   1407  CD  GLN   211       7.865  47.450  69.942  1.00  1.00
ATOM   1408  OE1 GLN   211       7.635  46.633  69.033  1.00  1.20
ATOM   1409  NE2 GLN   211       6.969  48.358  70.322  1.00  1.20
ATOM   1410  N   HIS   212      11.596  50.402  70.838  1.00  0.90
ATOM   1411  CA  HIS   212      11.626  51.404  71.890  1.00  0.90
ATOM   1412  C   HIS   212      11.372  52.818  71.352  1.00  0.90
ATOM   1413  O   HIS   212      10.613  53.603  71.948  1.00  0.90
ATOM   1414  CB  HIS   212      12.950  51.345  72.638  1.00  0.90
ATOM   1415  CG  HIS   212      13.062  52.314  73.821  1.00  1.00
ATOM   1416  ND1 HIS   212      13.365  53.672  73.612  1.00  1.00
ATOM   1417  CD2 HIS   212      12.806  52.092  75.097  1.00  1.20
ATOM   1418  CE1 HIS   212      13.318  54.304  74.830  1.00  1.20
ATOM   1419  NE2 HIS   212      12.977  53.329  75.762  1.00  1.50
ATOM   1420  N   LEU   213      11.993  53.142  70.218  1.00  0.90
ATOM   1421  CA  LEU   213      11.770  54.417  69.547  1.00  0.90
ATOM   1422  C   LEU   213      10.321  54.527  69.097  1.00  0.90
ATOM   1423  O   LEU   213       9.692  55.567  69.298  1.00  0.90
ATOM   1424  CB  LEU   213      12.761  54.618  68.362  1.00  0.90
ATOM   1425  CG  LEU   213      12.532  55.998  67.746  1.00  1.00
ATOM   1426  CD1 LEU   213      12.866  57.060  68.695  1.00  1.00
ATOM   1427  CD2 LEU   213      13.720  56.145  66.606  1.00  1.20
ATOM   1428  N   PHE   214       9.779  53.470  68.497  1.00  0.90
ATOM   1429  CA  PHE   214       8.378  53.507  68.066  1.00  0.90
ATOM   1430  C   PHE   214       7.431  53.702  69.282  1.00  0.90
ATOM   1431  O   PHE   214       6.675  54.666  69.344  1.00  0.90
ATOM   1432  CB  PHE   214       7.982  52.243  67.256  1.00  0.90
ATOM   1433  CG  PHE   214       8.767  52.185  65.934  1.00  1.00
ATOM   1434  CD1 PHE   214       9.141  53.404  65.354  1.00  1.00
ATOM   1435  CD2 PHE   214       8.674  51.074  65.129  1.00  1.20
ATOM   1436  CE1 PHE   214       9.623  53.407  64.060  1.00  1.20
ATOM   1437  CE2 PHE   214       9.164  51.041  63.850  1.00  1.50
ATOM   1438  CZ  PHE   214       9.674  52.250  63.306  1.00  1.50
ATOM   1439  N   GLU   215       7.510  52.827  70.267  1.00  0.90
ATOM   1440  CA  GLU   215       6.547  52.862  71.360  1.00  0.90
ATOM   1441  C   GLU   215       6.694  54.010  72.375  1.00  0.90
ATOM   1442  O   GLU   215       5.686  54.559  72.793  1.00  0.90
ATOM   1443  CB  GLU   215       6.402  51.473  72.003  1.00  0.90
ATOM   1444  CG  GLU   215       5.813  50.467  71.051  1.00  1.00
ATOM   1445  CD  GLU   215       4.343  50.815  70.650  1.00  1.00
ATOM   1446  OE1 GLU   215       3.533  51.255  71.481  1.00  1.20
ATOM   1447  OE2 GLU   215       4.013  50.583  69.455  1.00  1.20
ATOM   1448  N   ASP   216       7.921  54.369  72.754  1.00  0.90
ATOM   1449  CA  ASP   216       8.140  55.548  73.593  1.00  0.90
ATOM   1450  C   ASP   216       7.772  56.816  72.835  1.00  0.90
ATOM   1451  O   ASP   216       7.346  57.802  73.442  1.00  0.90
ATOM   1452  CB  ASP   216       9.578  55.632  74.104  1.00  0.90
ATOM   1453  CG  ASP   216       9.928  54.582  75.131  1.00  1.00
ATOM   1454  OD1 ASP   216       9.039  53.914  75.713  1.00  1.00
ATOM   1455  OD2 ASP   216      11.093  54.407  75.497  1.00  1.20
ATOM   1456  N   ILE   217       7.926  56.783  71.508  1.00  0.90
ATOM   1457  CA  ILE   217       7.534  57.873  70.637  1.00  0.90
ATOM   1458  C   ILE   217       6.035  58.083  70.570  1.00  0.90
ATOM   1459  O   ILE   217       5.564  59.213  70.642  1.00  0.90
ATOM   1460  CB  ILE   217       7.369  58.722  71.899  1.00  0.90
ATOM   1461  CG1 ILE   217       6.847  60.141  71.661  1.00  1.00
ATOM   1462  CG2 ILE   217       8.701  58.682  72.658  1.00  1.00
ATOM   1463  CD1 ILE   217       6.355  60.841  72.886  1.00  1.20
ATOM   1464  N   SER   218       3.950  57.472  70.907  1.00  0.90
ATOM   1465  CA  SER   218       2.488  57.448  70.857  1.00  0.90
ATOM   1466  C   SER   218       1.894  57.969  72.170  1.00  0.90
ATOM   1467  O   SER   218       0.971  58.772  72.153  1.00  0.90
ATOM   1468  CB  SER   218       1.953  56.011  70.577  1.00  0.90
ATOM   1469  OG  SER   218       0.429  56.006  70.452  1.00  1.00
TER
END
