
#######################################################
#                                                     #
#                        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   11 (   55),  selected   11 , name T0386TS103_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   11 , name T0386_D2.pdb
# PARAMETERS: T0386TS103_1-D2.T0386_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:    11       219 - 232         2.55     2.55
  LCS_AVERAGE:     13.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       225 - 232         0.54     3.03
  LCS_AVERAGE:      8.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       225 - 232         0.54     3.03
  LCS_AVERAGE:      8.19

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:   81
LCS_GDT     N     219     N     219      3    4   11     3    3    3    3    3    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     P     220     P     220      3    4   11     3    3    3    3    3    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     221     E     221      3    4   11     3    3    3    3    3    4    9   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     225     L     225      8    8   11     4    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     226     L     226      8    8   11     6    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     K     227     K     227      8    8   11     6    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     228     E     228      8    8   11     6    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     F     229     F     229      8    8   11     6    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     M     230     M     230      8    8   11     6    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     H     231     H     231      8    8   11     6    8    8    8    8    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     T     232     T     232      8    8   11     3    8    8    8    8    8   10   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:  10.10  (   8.19    8.53   13.58 )

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      8      8      8      9     10     11     11     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   7.41   9.88   9.88   9.88   9.88  11.11  12.35  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58
GDT RMS_LOCAL    0.23   0.54   0.54   0.54   0.54   2.09   2.11   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55
GDT RMS_ALL_CA   3.05   3.03   3.03   3.03   3.03   2.61   2.63   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55   2.55

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          2.888
LGA    P     220      P     220          2.646
LGA    E     221      E     221          3.822
LGA    L     225      L     225          2.346
LGA    L     226      L     226          2.568
LGA    K     227      K     227          1.970
LGA    E     228      E     228          2.410
LGA    F     229      F     229          2.661
LGA    M     230      M     230          2.102
LGA    H     231      H     231          2.656
LGA    T     232      T     232          3.970

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   81    4.0     11    2.55    11.728    11.023     0.415

LGA_LOCAL      RMSD =  2.549  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.797  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  2.549  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.994899 * X  +  -0.089897 * Y  +   0.045760 * Z  +   8.013777
  Y_new =  -0.100366 * X  +   0.927646 * Y  +  -0.359723 * Z  +   5.546304
  Z_new =  -0.010111 * X  +  -0.362481 * Y  +  -0.931937 * Z  +  94.266701 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.770645    0.370948  [ DEG:  -158.7462     21.2538 ]
  Theta =   0.010111    3.131481  [ DEG:     0.5793    179.4207 ]
  Phi   =  -3.041052    0.100540  [ DEG:  -174.2395      5.7605 ]
 
# 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: T0386TS103_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS103_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   81   4.0   11   2.55  11.023     2.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS103_1-D2
PFRMAT TS
TARGET T0386
MODEL 1
PARENT 2g03_A
ATOM    734  N   ASN   219       5.806  56.622  75.110  1.00  1.00
ATOM    735  CA  ASN   219       4.879  57.205  76.055  1.00  1.00
ATOM    736  C   ASN   219       4.798  58.733  75.886  1.00  1.00
ATOM    737  O   ASN   219       5.817  59.423  75.888  1.00  1.00
ATOM    738  CB  ASN   219       5.314  56.815  77.448  1.00  1.00
ATOM    739  N   PRO   220       3.587  59.252  75.700  1.00  1.00
ATOM    740  CA  PRO   220       3.388  60.685  75.481  1.00  1.00
ATOM    741  C   PRO   220       4.001  61.569  76.588  1.00  1.00
ATOM    742  O   PRO   220       4.605  62.595  76.292  1.00  1.00
ATOM    743  CB  PRO   220       1.900  61.010  75.265  1.00  1.00
ATOM    744  N   GLU   221       3.873  61.161  77.846  1.00  1.00
ATOM    745  CA  GLU   221       4.370  61.960  78.953  1.00  1.00
ATOM    746  C   GLU   221       5.904  62.006  78.993  1.00  1.00
ATOM    747  O   GLU   221       6.506  63.072  79.210  1.00  1.00
ATOM    748  CB  GLU   221       3.815  61.438  80.272  1.00  1.00
ATOM    749  N   LEU   225       6.539  60.856  78.771  1.00  1.00
ATOM    750  CA  LEU   225       7.991  60.772  78.688  1.00  1.00
ATOM    751  C   LEU   225       8.497  61.587  77.507  1.00  1.00
ATOM    752  O   LEU   225       9.464  62.338  77.646  1.00  1.00
ATOM    753  CB  LEU   225       8.475  59.293  78.621  1.00  1.00
ATOM    754  N   LEU   226       7.857  61.457  76.347  1.00  1.00
ATOM    755  CA  LEU   226       8.280  62.237  75.180  1.00  1.00
ATOM    756  C   LEU   226       8.138  63.760  75.453  1.00  1.00
ATOM    757  O   LEU   226       9.110  64.506  75.390  1.00  1.00
ATOM    758  CB  LEU   226       7.510  61.831  73.895  1.00  1.00
ATOM    759  N   LYS   227       6.948  64.209  75.808  1.00  1.00
ATOM    760  CA  LYS   227       6.710  65.642  75.926  1.00  1.00
ATOM    761  C   LYS   227       7.336  66.350  77.142  1.00  1.00
ATOM    762  O   LYS   227       7.833  67.455  76.988  1.00  1.00
ATOM    763  CB  LYS   227       5.223  65.967  75.709  1.00  1.00
ATOM    764  N   GLU   228       7.319  65.724  78.318  1.00  1.00
ATOM    765  CA  GLU   228       8.029  66.268  79.477  1.00  1.00
ATOM    766  C   GLU   228       9.533  66.238  79.240  1.00  1.00
ATOM    767  O   GLU   228      10.260  67.091  79.757  1.00  1.00
ATOM    768  CB  GLU   228       7.678  65.529  80.767  1.00  1.00
ATOM    769  N   PHE   229       9.992  65.263  78.451  1.00  1.00
ATOM    770  CA  PHE   229      11.383  65.152  78.056  1.00  1.00
ATOM    771  C   PHE   229      11.838  66.265  77.135  1.00  1.00
ATOM    772  O   PHE   229      12.911  66.827  77.326  1.00  1.00
ATOM    773  CB  PHE   229      11.550  63.821  77.300  1.00  1.00
ATOM    774  N   MET   230      11.049  66.558  76.103  1.00  1.00
ATOM    775  CA  MET   230      11.281  67.698  75.217  1.00  1.00
ATOM    776  C   MET   230      11.324  69.005  76.019  1.00  1.00
ATOM    777  O   MET   230      12.203  69.829  75.807  1.00  1.00
ATOM    778  CB  MET   230      10.181  67.797  74.118  1.00  1.00
ATOM    779  N   HIS   231      10.373  69.202  76.923  1.00  1.00
ATOM    780  CA  HIS   231      10.422  70.372  77.793  1.00  1.00
ATOM    781  C   HIS   231      11.704  70.468  78.627  1.00  1.00
ATOM    782  O   HIS   231      12.237  71.556  78.796  1.00  1.00
ATOM    783  CB  HIS   231       9.221  70.452  78.707  1.00  1.00
ATOM    784  N   THR   232      12.182  69.345  79.154  1.00  1.00
ATOM    785  CA  THR   232      13.385  69.355  79.975  1.00  1.00
ATOM    786  C   THR   232      14.607  69.629  79.101  1.00  1.00
ATOM    787  O   THR   232      15.444  70.440  79.451  1.00  1.00
ATOM    788  CB  THR   232      13.528  68.040  80.758  1.00  1.00
TER
END
