
#######################################################
#                                                     #
#                        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 T0378TS247_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_3-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          3.33     3.33
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.47     3.72
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.70     4.61
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.93     3.62
  LCS_AVERAGE:      5.30

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    6    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    6    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    6    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    6    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    6    7    7    7    7    7    7    7 
LCS_GDT     F      88     F      88      5    6    7     3    3    5    5    6    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7 
LCS_GDT     D      89     D      89      3    3    7     0    3    3    3    3    4    4    4    4    4    6    6    6    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   6.47  (   5.30    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      6      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   6.74   7.87   7.87   7.87   7.87   7.87   7.87   7.87
GDT RMS_LOCAL    0.13   0.70   0.70   0.70   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   3.33   3.33   3.33   3.33   3.33   3.33   3.33
GDT RMS_ALL_CA   4.11   4.61   4.61   4.61   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.33   3.33   3.33   3.33   3.33   3.33   3.33

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          2.088
LGA    L      84      L      84          1.181
LGA    M      85      M      85          0.484
LGA    A      86      A      86          1.021
LGA    V      87      V      87          0.714
LGA    F      88      F      88          2.339
LGA    D      89      D      89          9.166

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.47     6.461     6.473     0.382

LGA_LOCAL      RMSD =  1.473  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.723  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.331  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.908066 * X  +   0.072580 * Y  +   0.412490 * Z  +   0.796882
  Y_new =   0.294112 * X  +   0.590675 * Y  +  -0.751399 * Z  +  24.836336
  Z_new =  -0.298184 * X  +   0.803639 * Y  +   0.515025 * Z  +  40.336582 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.000868   -2.140724  [ DEG:    57.3455   -122.6545 ]
  Theta =   0.302790    2.838803  [ DEG:    17.3486    162.6514 ]
  Phi   =   0.313226   -2.828366  [ DEG:    17.9466   -162.0534 ]
 
# 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: T0378TS247_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_3-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   1.47   6.473     3.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_3-D1
PFRMAT TS
TARGET T0378
MODEL  3
PARENT 1zjr_A 1gz0_A 1gz0_B 1gz0_C 1gz0_D 1gz0_F 1gz0_H 1v2x_A 1x7p_A 1ipa_A
ATOM      1  N   PRO    83       0.797  24.836  40.337  1.00 0.00         0
ATOM      2  CA  PRO    83       1.395  23.747  41.083  1.00 0.00         0
ATOM      3  C   PRO    83       1.659  24.332  42.464  1.00 0.00         0
ATOM      4  O   PRO    83       2.404  25.306  42.570  1.00 0.00         0
ATOM      5  CB  PRO    83       2.662  23.409  40.294  1.00 0.00         0
ATOM      6  CG  PRO    83       2.372  23.872  38.906  1.00 0.00         0
ATOM      7  CD  PRO    83       1.554  25.126  39.048  1.00 0.00         0
ATOM      8  N   LEU    84       1.061  23.750  43.501  1.00 0.00         0
ATOM      9  CA  LEU    84       1.242  24.249  44.855  1.00 0.00         0
ATOM     10  C   LEU    84       2.403  23.516  45.506  1.00 0.00         0
ATOM     11  O   LEU    84       2.419  22.288  45.589  1.00 0.00         0
ATOM     12  CB  LEU    84      -0.023  24.019  45.685  1.00 0.00         0
ATOM     13  CG  LEU    84       0.032  24.471  47.145  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.193  25.981  47.235  1.00 0.00         0
ATOM     15  CD2 LEU    84      -1.244  24.085  47.876  1.00 0.00         0
ATOM     16  N   MET    85       3.386  24.286  45.972  1.00 0.00         0
ATOM     17  CA  MET    85       4.545  23.709  46.629  1.00 0.00         0
ATOM     18  C   MET    85       4.268  23.455  48.106  1.00 0.00         0
ATOM     19  O   MET    85       3.667  24.273  48.809  1.00 0.00         0
ATOM     20  CB  MET    85       5.745  24.653  46.525  1.00 0.00         0
ATOM     21  CG  MET    85       6.211  24.910  45.102  1.00 0.00         0
ATOM     22  SD  MET    85       6.698  23.400  44.245  1.00 0.00         0
ATOM     23  CE  MET    85       8.172  22.954  45.158  1.00 0.00         0
ATOM     24  N   ALA    86       4.720  22.294  48.575  1.00 0.00         0
ATOM     25  CA  ALA    86       4.626  21.933  49.980  1.00 0.00         0
ATOM     26  C   ALA    86       6.019  21.710  50.556  1.00 0.00         0
ATOM     27  O   ALA    86       6.972  21.485  49.806  1.00 0.00         0
ATOM     28  CB  ALA    86       3.820  20.655  50.146  1.00 0.00         0
ATOM     29  N   VAL    87       6.129  21.774  51.891  1.00 0.00         0
ATOM     30  CA  VAL    87       7.366  21.573  52.650  1.00 0.00         0
ATOM     31  C   VAL    87       8.313  20.467  52.166  1.00 0.00         0
ATOM     32  O   VAL    87       9.535  20.645  52.141  1.00 0.00         0
ATOM     33  CB  VAL    87       7.075  21.207  54.118  1.00 0.00         0
ATOM     34  CG1 VAL    87       6.416  19.840  54.205  1.00 0.00         0
ATOM     35  CG2 VAL    87       8.364  21.173  54.924  1.00 0.00         0
ATOM     36  N   PHE    88       7.758  19.314  51.777  1.00 0.00         0
ATOM     37  CA  PHE    88       8.525  18.198  51.240  1.00 0.00         0
ATOM     38  C   PHE    88       9.223  18.527  49.918  1.00 0.00         0
ATOM     39  O   PHE    88      10.354  18.103  49.673  1.00 0.00         0
ATOM     40  CB  PHE    88       7.613  16.998  50.977  1.00 0.00         0
ATOM     41  CG  PHE    88       8.328  15.805  50.413  1.00 0.00         0
ATOM     42  CD1 PHE    88       9.064  14.968  51.235  1.00 0.00         0
ATOM     43  CD2 PHE    88       8.266  15.516  49.062  1.00 0.00         0
ATOM     44  CE1 PHE    88       9.723  13.871  50.717  1.00 0.00         0
ATOM     45  CE2 PHE    88       8.925  14.418  48.543  1.00 0.00         0
ATOM     46  CZ  PHE    88       9.651  13.596  49.365  1.00 0.00         0
ATOM     47  N   ASP    89       8.563  19.289  49.042  1.00 0.00         0
ATOM     48  CA  ASP    89       9.082  19.543  47.703  1.00 0.00         0
ATOM     49  C   ASP    89      10.073  20.699  47.641  1.00 0.00         0
ATOM     50  O   ASP    89      10.556  21.059  46.566  1.00 0.00         0
ATOM     51  CB  ASP    89       7.942  19.886  46.743  1.00 0.00         0
ATOM     52  CG  ASP    89       7.075  18.687  46.415  1.00 0.00         0
ATOM     53  OD1 ASP    89       7.506  17.549  46.692  1.00 0.00         0
ATOM     54  OD2 ASP    89       5.964  18.885  45.880  1.00 0.00         0
TER
END
