
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_4-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          3.41     3.41
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.44     3.79
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.49     4.65
  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    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      3    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    3    4    4    4    4    6    6    6    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      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    0.17   0.49   0.49   0.49   1.44   1.44   1.44   1.44   1.44   1.44   1.44   1.44   1.44   3.41   3.41   3.41   3.41   3.41   3.41   3.41
GDT RMS_ALL_CA   4.25   4.65   4.65   4.65   3.79   3.79   3.79   3.79   3.79   3.79   3.79   3.79   3.79   3.41   3.41   3.41   3.41   3.41   3.41   3.41

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          1.851
LGA    L      84      L      84          0.929
LGA    M      85      M      85          0.675
LGA    A      86      A      86          1.259
LGA    V      87      V      87          0.588
LGA    F      88      F      88          2.386
LGA    D      89      D      89          9.389

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.44     6.461     6.473     0.391

LGA_LOCAL      RMSD =  1.436  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.789  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.415  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.993582 * X  +  -0.038691 * Y  +   0.106293 * Z  +   1.445270
  Y_new =   0.110814 * X  +   0.521552 * Y  +  -0.845993 * Z  +  25.429205
  Z_new =  -0.022705 * X  +   0.852342 * Y  +   0.522492 * Z  +  40.095551 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.020868   -2.120725  [ DEG:    58.4914   -121.5086 ]
  Theta =   0.022707    3.118886  [ DEG:     1.3010    178.6990 ]
  Phi   =   0.111071   -3.030522  [ DEG:     6.3639   -173.6361 ]
 
# 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_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_4-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   1.44   6.473     3.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
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       1.445  25.429  40.096  1.00 0.00         0
ATOM      2  CA  PRO    83       1.600  24.201  40.854  1.00 0.00         0
ATOM      3  C   PRO    83       1.585  24.629  42.316  1.00 0.00         0
ATOM      4  O   PRO    83       1.926  25.785  42.595  1.00 0.00         0
ATOM      5  CB  PRO    83       2.945  23.643  40.386  1.00 0.00         0
ATOM      6  CG  PRO    83       3.149  24.246  39.036  1.00 0.00         0
ATOM      7  CD  PRO    83       2.578  25.633  39.108  1.00 0.00         0
ATOM      8  N   LEU    84       1.207  23.743  43.236  1.00 0.00         0
ATOM      9  CA  LEU    84       1.149  24.068  44.654  1.00 0.00         0
ATOM     10  C   LEU    84       2.237  23.290  45.377  1.00 0.00         0
ATOM     11  O   LEU    84       2.383  22.082  45.161  1.00 0.00         0
ATOM     12  CB  LEU    84      -0.215  23.690  45.235  1.00 0.00         0
ATOM     13  CG  LEU    84      -1.431  24.381  44.615  1.00 0.00         0
ATOM     14  CD1 LEU    84      -2.720  23.851  45.225  1.00 0.00         0
ATOM     15  CD2 LEU    84      -1.375  25.883  44.852  1.00 0.00         0
ATOM     16  N   MET    85       3.015  23.955  46.238  1.00 0.00         0
ATOM     17  CA  MET    85       4.175  23.319  46.850  1.00 0.00         0
ATOM     18  C   MET    85       4.065  23.215  48.362  1.00 0.00         0
ATOM     19  O   MET    85       3.732  24.183  49.050  1.00 0.00         0
ATOM     20  CB  MET    85       5.446  24.114  46.543  1.00 0.00         0
ATOM     21  CG  MET    85       6.704  23.539  47.173  1.00 0.00         0
ATOM     22  SD  MET    85       8.193  24.440  46.700  1.00 0.00         0
ATOM     23  CE  MET    85       7.941  25.989  47.564  1.00 0.00         0
ATOM     24  N   ALA    86       4.349  22.022  48.887  1.00 0.00         0
ATOM     25  CA  ALA    86       4.484  21.817  50.322  1.00 0.00         0
ATOM     26  C   ALA    86       5.958  21.752  50.717  1.00 0.00         0
ATOM     27  O   ALA    86       6.824  21.639  49.850  1.00 0.00         0
ATOM     28  CB  ALA    86       3.817  20.516  50.737  1.00 0.00         0
ATOM     29  N   VAL    87       6.261  21.824  52.023  1.00 0.00         0
ATOM     30  CA  VAL    87       7.616  21.711  52.575  1.00 0.00         0
ATOM     31  C   VAL    87       8.510  20.622  51.966  1.00 0.00         0
ATOM     32  O   VAL    87       9.689  20.851  51.683  1.00 0.00         0
ATOM     33  CB  VAL    87       7.587  21.397  54.082  1.00 0.00         0
ATOM     34  CG1 VAL    87       7.022  20.006  54.326  1.00 0.00         0
ATOM     35  CG2 VAL    87       8.991  21.455  54.666  1.00 0.00         0
ATOM     36  N   PHE    88       7.955  19.424  51.759  1.00 0.00         0
ATOM     37  CA  PHE    88       8.676  18.293  51.182  1.00 0.00         0
ATOM     38  C   PHE    88       9.087  18.508  49.729  1.00 0.00         0
ATOM     39  O   PHE    88      10.042  17.909  49.233  1.00 0.00         0
ATOM     40  CB  PHE    88       7.810  17.032  51.215  1.00 0.00         0
ATOM     41  CG  PHE    88       7.646  16.446  52.588  1.00 0.00         0
ATOM     42  CD1 PHE    88       6.484  16.653  53.311  1.00 0.00         0
ATOM     43  CD2 PHE    88       8.654  15.686  53.157  1.00 0.00         0
ATOM     44  CE1 PHE    88       6.334  16.113  54.574  1.00 0.00         0
ATOM     45  CE2 PHE    88       8.503  15.146  54.420  1.00 0.00         0
ATOM     46  CZ  PHE    88       7.350  15.357  55.128  1.00 0.00         0
ATOM     47  N   ASP    89       8.353  19.379  49.030  1.00 0.00         0
ATOM     48  CA  ASP    89       8.588  19.637  47.619  1.00 0.00         0
ATOM     49  C   ASP    89       9.623  20.733  47.406  1.00 0.00         0
ATOM     50  O   ASP    89      10.042  20.959  46.270  1.00 0.00         0
ATOM     51  CB  ASP    89       7.294  20.081  46.933  1.00 0.00         0
ATOM     52  CG  ASP    89       6.231  19.001  46.939  1.00 0.00         0
ATOM     53  OD1 ASP    89       6.555  17.845  46.593  1.00 0.00         0
ATOM     54  OD2 ASP    89       5.073  19.309  47.291  1.00 0.00         0
TER
END
