
#######################################################
#                                                     #
#                        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    7 (   54),  selected    7 , name T0378TS302_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_5-D1.T0378_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:     7        83 - 89          3.43     3.43
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.46     3.81
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.50     4.67
  LCS_AVERAGE:      4.98

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:   89
LCS_GDT     P      83     P      83      5    6    7     3    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     L      84     L      84      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     M      85     M      85      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     A      86     A      86      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     V      87     V      87      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     F      88     F      88      3    6    7     0    3    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     D      89     D      89      3    3    7     0    3    3    3    3    3    4    4    4    4    6    6    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   6.37  (   4.98    6.26    7.87 )

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      5      5      5      6      6      6      6      6      6      6      6      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   4.49   5.62   5.62   5.62   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87
GDT RMS_LOCAL    0.12   0.50   0.50   0.50   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43
GDT RMS_ALL_CA   4.28   4.67   4.67   4.67   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          1.898
LGA    L      84      L      84          1.040
LGA    M      85      M      85          0.555
LGA    A      86      A      86          1.138
LGA    V      87      V      87          0.570
LGA    F      88      F      88          2.471
LGA    D      89      D      89          9.435

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.46     6.461     6.508     0.386

LGA_LOCAL      RMSD =  1.456  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.812  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.434  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.383372 * X  +  -0.226527 * Y  +   0.895383 * Z  +  39.544395
  Y_new =  -0.168470 * X  +  -0.936039 * Y  +  -0.308946 * Z  + 116.017754
  Z_new =   0.908099 * X  +  -0.269287 * Y  +   0.320689 * Z  +  46.766342 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.698493    2.443100  [ DEG:   -40.0207    139.9793 ]
  Theta =  -1.138721   -2.002872  [ DEG:   -65.2439   -114.7561 ]
  Phi   =  -2.727553    0.414040  [ DEG:  -156.2773     23.7227 ]
 
# 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: T0378TS302_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_5-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   89   4.0    6   1.46   6.508     3.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_5-D1
PFRMAT TS
TARGET T0378
MODEL  5
PARENT 1gz0_D
ATOM   1000  N   PRO    83       1.450  25.342  40.330  1.00  0.00
ATOM   1000  CA  PRO    83       1.605  24.112  41.084  1.00  0.00
ATOM   1000  C   PRO    83       1.697  24.544  42.510  1.00  0.00
ATOM   1000  O   PRO    83       2.087  25.683  42.753  1.00  0.00
ATOM   1000  CB  PRO    83       2.956  23.522  40.632  1.00  0.00
ATOM   1000  CG  PRO    83       3.738  24.684  39.937  1.00  0.00
ATOM   1000  CD  PRO    83       2.698  25.809  39.709  1.00  0.00
ATOM   1000  N   LEU    84       1.408  23.651  43.458  1.00  0.00
ATOM   1000  CA  LEU    84       1.287  24.100  44.816  1.00  0.00
ATOM   1000  C   LEU    84       2.374  23.270  45.359  1.00  0.00
ATOM   1000  O   LEU    84       2.643  22.198  44.815  1.00  0.00
ATOM   1000  CB  LEU    84      -0.028  23.823  45.578  1.00  0.00
ATOM   1000  CG  LEU    84      -0.995  25.035  45.729  1.00  0.00
ATOM   1000  CD1 LEU    84      -2.027  24.779  46.844  1.00  0.00
ATOM   1000  CD2 LEU    84      -0.306  26.406  45.938  1.00  0.00
ATOM   1000  N   MET    85       3.042  23.772  46.402  1.00  0.00
ATOM   1000  CA  MET    85       4.323  23.259  46.763  1.00  0.00
ATOM   1000  C   MET    85       4.144  23.188  48.218  1.00  0.00
ATOM   1000  O   MET    85       3.598  24.109  48.829  1.00  0.00
ATOM   1000  CB  MET    85       5.553  24.118  46.440  1.00  0.00
ATOM   1000  CG  MET    85       5.861  24.153  44.942  1.00  0.00
ATOM   1000  SD  MET    85       6.221  22.533  44.191  1.00  0.00
ATOM   1000  CE  MET    85       6.303  23.163  42.492  1.00  0.00
ATOM   1000  N   ALA    86       4.566  22.050  48.773  1.00  0.00
ATOM   1000  CA  ALA    86       4.462  21.781  50.169  1.00  0.00
ATOM   1000  C   ALA    86       5.882  21.858  50.594  1.00  0.00
ATOM   1000  O   ALA    86       6.769  22.046  49.763  1.00  0.00
ATOM   1000  CB  ALA    86       3.930  20.375  50.501  1.00  0.00
ATOM   1000  N   VAL    87       6.130  21.712  51.911  1.00  0.00
ATOM   1000  CA  VAL    87       7.442  21.735  52.498  1.00  0.00
ATOM   1000  C   VAL    87       8.353  20.729  51.841  1.00  0.00
ATOM   1000  O   VAL    87       9.541  20.987  51.651  1.00  0.00
ATOM   1000  CB  VAL    87       7.378  21.561  54.005  1.00  0.00
ATOM   1000  CG1 VAL    87       6.725  20.217  54.409  1.00  0.00
ATOM   1000  CG2 VAL    87       8.763  21.796  54.640  1.00  0.00
ATOM   1000  N   PHE    88       7.796  19.596  51.389  1.00  0.00
ATOM   1000  CA  PHE    88       8.581  18.421  51.108  1.00  0.00
ATOM   1000  C   PHE    88       9.053  18.629  49.690  1.00  0.00
ATOM   1000  O   PHE    88       9.968  17.961  49.214  1.00  0.00
ATOM   1000  CB  PHE    88       7.726  17.132  51.198  1.00  0.00
ATOM   1000  CG  PHE    88       8.433  15.886  50.750  1.00  0.00
ATOM   1000  CD1 PHE    88       9.403  15.315  51.540  1.00  0.00
ATOM   1000  CD2 PHE    88       8.163  15.317  49.518  1.00  0.00
ATOM   1000  CE1 PHE    88      10.108  14.215  51.120  1.00  0.00
ATOM   1000  CE2 PHE    88       8.873  14.210  49.102  1.00  0.00
ATOM   1000  CZ  PHE    88       9.764  13.593  49.941  1.00  0.00
ATOM   1000  N   ASP    89       8.464  19.623  49.002  1.00  0.00
ATOM   1000  CA  ASP    89       8.633  19.769  47.591  1.00  0.00
ATOM   1000  C   ASP    89       9.668  20.817  47.419  1.00  0.00
ATOM   1000  O   ASP    89      10.063  21.070  46.285  1.00  0.00
ATOM   1000  CB  ASP    89       7.427  20.337  46.822  1.00  0.00
ATOM   1000  CG  ASP    89       6.313  19.314  46.759  1.00  0.00
ATOM   1000  OD1 ASP    89       6.580  18.105  46.991  1.00  0.00
ATOM   1000  OD2 ASP    89       5.157  19.742  46.502  1.00  0.00
TER
END
