
#######################################################
#                                                     #
#                        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 (   77),  selected   10 , name T0378TS401_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   10 , name T0378_D1.pdb
# PARAMETERS: T0378TS401_2-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:     9        80 - 88          4.71     5.39
  LONGEST_CONTINUOUS_SEGMENT:     9        81 - 89          4.74     5.47
  LCS_AVERAGE:     10.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.98     8.40
  LCS_AVERAGE:      3.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.98     8.40
  LCS_AVERAGE:      3.82

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     T      80     T      80      3    3    9     0    3    3    3    3    4    4    4    6    6    7    9    9    9   10   10   10   10   10   10 
LCS_GDT     P      81     P      81      3    3    9     0    3    3    3    4    4    5    5    6    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     Q      82     Q      82      4    4    9     3    3    4    4    4    4    5    5    6    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     P      83     P      83      4    4    9     3    3    4    4    4    4    5    5    6    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     L      84     L      84      4    4    9     3    3    4    4    4    4    5    5    6    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     M      85     M      85      4    4    9     0    3    4    4    4    4    5    5    6    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     A      86     A      86      3    3    9     0    3    3    3    3    3    4    5    6    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     V      87     V      87      3    3    9     1    3    3    3    3    3    4    4    5    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     F      88     F      88      3    3    9     0    3    3    3    3    3    4    4    5    6    8    9    9    9   10   10   10   10   10   10 
LCS_GDT     D      89     D      89      3    3    9     0    3    3    3    3    3    4    4    4    6    6    7    8    9   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   5.92  (   3.82    3.82   10.11 )

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      3      3      4      4      4      4      5      5      6      6      8      9      9      9     10     10     10     10     10     10 
GDT PERCENT_CA   3.37   3.37   4.49   4.49   4.49   4.49   5.62   5.62   6.74   6.74   8.99  10.11  10.11  10.11  11.24  11.24  11.24  11.24  11.24  11.24
GDT RMS_LOCAL    0.17   0.17   0.98   0.98   0.98   0.98   2.38   2.38   3.10   3.10   4.31   4.71   4.71   4.71   5.18   5.18   5.18   5.18   5.18   5.18
GDT RMS_ALL_CA   8.96   8.96   8.40   8.40   8.40   8.40   7.46   7.46   7.62   7.62   5.53   5.39   5.39   5.39   5.18   5.18   5.18   5.18   5.18   5.18

#      Molecule1      Molecule2       DISTANCE
LGA    T      80      T      80          7.347
LGA    P      81      P      81          3.208
LGA    Q      82      Q      82          3.052
LGA    P      83      P      83          0.578
LGA    L      84      L      84          2.028
LGA    M      85      M      85          2.088
LGA    A      86      A      86          8.020
LGA    V      87      V      87         11.027
LGA    F      88      F      88         10.199
LGA    D      89      D      89         13.567

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10   89    4.0      5    2.38     6.180     5.706     0.201

LGA_LOCAL      RMSD =  2.384  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.459  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  5.178  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.264774 * X  +   0.258607 * Y  +  -0.928987 * Z  +   9.108339
  Y_new =  -0.111028 * X  +  -0.948787 * Y  +  -0.295763 * Z  +  40.749649
  Z_new =  -0.957897 * X  +   0.181454 * Y  +  -0.222501 * Z  +  72.579330 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.457461   -0.684132  [ DEG:   140.8021    -39.1979 ]
  Theta =   1.279587    1.862005  [ DEG:    73.3150    106.6850 ]
  Phi   =  -0.397059    2.744533  [ DEG:   -22.7498    157.2502 ]
 
# 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: T0378TS401_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS401_2-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10   89   4.0    5   2.38   5.706     5.18
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS401_2-D1
PFRMAT TS
TARGET T0378
MODEL  2 REFINED
PARENT 1v2x_A
ATOM      1  N   THR    80       2.410  23.100  35.948  1.00114.65       1SG   2
ATOM      2  CA  THR    80       2.174  22.490  37.276  1.00114.65       1SG   3
ATOM      3  CB  THR    80       2.153  20.990  37.175  1.00114.65       1SG   4
ATOM      4  OG1 THR    80       1.822  20.425  38.435  1.00114.65       1SG   5
ATOM      5  CG2 THR    80       3.518  20.471  36.698  1.00114.65       1SG   6
ATOM      6  C   THR    80       3.128  22.898  38.356  1.00114.65       1SG   7
ATOM      7  O   THR    80       2.805  22.679  39.518  1.00114.65       1SG   8
ATOM      8  N   PRO    81       4.288  23.447  38.114  1.00 95.24       1SG   9
ATOM      9  CA  PRO    81       5.042  23.861  39.261  1.00 95.24       1SG  10
ATOM     10  CD  PRO    81       5.168  22.980  37.051  1.00 95.24       1SG  11
ATOM     11  CB  PRO    81       6.456  24.131  38.758  1.00 95.24       1SG  12
ATOM     12  CG  PRO    81       6.601  23.154  37.578  1.00 95.24       1SG  13
ATOM     13  C   PRO    81       4.393  25.010  39.960  1.00 95.24       1SG  14
ATOM     14  O   PRO    81       4.572  25.147  41.170  1.00 95.24       1SG  15
ATOM     15  N   GLN    82       3.654  25.866  39.226  1.00 99.31       1SG  16
ATOM     16  CA  GLN    82       3.054  26.991  39.876  1.00 99.31       1SG  17
ATOM     17  CB  GLN    82       2.450  28.006  38.883  1.00 99.31       1SG  18
ATOM     18  CG  GLN    82       3.482  28.598  37.921  1.00 99.31       1SG  19
ATOM     19  CD  GLN    82       2.745  29.444  36.892  1.00 99.31       1SG  20
ATOM     20  OE1 GLN    82       2.283  30.546  37.183  1.00 99.31       1SG  21
ATOM     21  NE2 GLN    82       2.632  28.908  35.647  1.00 99.31       1SG  22
ATOM     22  C   GLN    82       1.985  26.498  40.805  1.00 99.31       1SG  23
ATOM     23  O   GLN    82       1.930  26.927  41.956  1.00 99.31       1SG  24
ATOM     24  N   PRO    83       1.113  25.624  40.369  1.00 84.37       1SG  25
ATOM     25  CA  PRO    83       0.130  25.098  41.272  1.00 84.37       1SG  26
ATOM     26  CD  PRO    83       0.644  25.595  38.993  1.00 84.37       1SG  27
ATOM     27  CB  PRO    83      -1.015  24.559  40.408  1.00 84.37       1SG  28
ATOM     28  CG  PRO    83      -0.438  24.509  38.981  1.00 84.37       1SG  29
ATOM     29  C   PRO    83       0.715  24.086  42.191  1.00 84.37       1SG  30
ATOM     30  O   PRO    83       0.176  23.885  43.273  1.00 84.37       1SG  31
ATOM     31  N   LEU    84       1.789  23.397  41.788  1.00132.55       1SG  32
ATOM     32  CA  LEU    84       2.329  22.373  42.625  1.00132.55       1SG  33
ATOM     33  CB  LEU    84       3.437  21.557  41.943  1.00132.55       1SG  34
ATOM     34  CG  LEU    84       3.967  20.404  42.814  1.00132.55       1SG  35
ATOM     35  CD2 LEU    84       5.243  19.791  42.218  1.00132.55       1SG  36
ATOM     36  CD1 LEU    84       2.869  19.357  43.067  1.00132.55       1SG  37
ATOM     37  C   LEU    84       2.916  23.026  43.829  1.00132.55       1SG  38
ATOM     38  O   LEU    84       2.703  22.578  44.952  1.00132.55       1SG  39
ATOM     39  N   MET    85       3.722  24.082  43.608  1.00 45.94       1SG  40
ATOM     40  CA  MET    85       4.311  24.802  44.697  1.00 45.94       1SG  41
ATOM     41  CB  MET    85       5.360  25.827  44.233  1.00 45.94       1SG  42
ATOM     42  CG  MET    85       6.614  25.199  43.624  1.00 45.94       1SG  43
ATOM     43  SD  MET    85       7.853  26.402  43.055  1.00 45.94       1SG  44
ATOM     44  CE  MET    85       8.289  26.995  44.715  1.00 45.94       1SG  45
ATOM     45  C   MET    85       3.263  25.573  45.438  1.00 45.94       1SG  46
ATOM     46  O   MET    85       3.160  25.491  46.659  1.00 45.94       1SG  47
ATOM     47  N   ALA    86       2.431  26.328  44.693  1.00 41.13       1SG  48
ATOM     48  CA  ALA    86       1.469  27.195  45.312  1.00 41.13       1SG  49
ATOM     49  CB  ALA    86       0.710  28.064  44.296  1.00 41.13       1SG  50
ATOM     50  C   ALA    86       0.454  26.391  46.054  1.00 41.13       1SG  51
ATOM     51  O   ALA    86       0.139  26.686  47.206  1.00 41.13       1SG  52
ATOM     52  N   VAL    87      -0.078  25.338  45.410  1.00 95.50       1SG  53
ATOM     53  CA  VAL    87      -1.095  24.552  46.041  1.00 95.50       1SG  54
ATOM     54  CB  VAL    87      -1.765  23.512  45.172  1.00 95.50       1SG  55
ATOM     55  CG1 VAL    87      -0.927  22.219  45.127  1.00 95.50       1SG  56
ATOM     56  CG2 VAL    87      -3.192  23.297  45.705  1.00 95.50       1SG  57
ATOM     57  C   VAL    87      -0.479  23.842  47.194  1.00 95.50       1SG  58
ATOM     58  O   VAL    87      -1.110  23.664  48.227  1.00 95.50       1SG  59
ATOM     59  N   PHE    88       0.768  23.369  47.058  1.00 99.01       1SG  60
ATOM     60  CA  PHE    88       1.319  22.682  48.185  1.00 99.01       1SG  61
ATOM     61  CB  PHE    88       2.667  21.999  47.909  1.00 99.01       1SG  62
ATOM     62  CG  PHE    88       3.156  21.544  49.239  1.00 99.01       1SG  63
ATOM     63  CD1 PHE    88       2.617  20.433  49.847  1.00 99.01       1SG  64
ATOM     64  CD2 PHE    88       4.159  22.233  49.880  1.00 99.01       1SG  65
ATOM     65  CE1 PHE    88       3.074  20.020  51.077  1.00 99.01       1SG  66
ATOM     66  CE2 PHE    88       4.618  21.823  51.109  1.00 99.01       1SG  67
ATOM     67  CZ  PHE    88       4.077  20.712  51.710  1.00 99.01       1SG  68
ATOM     68  C   PHE    88       1.538  23.643  49.307  1.00 99.01       1SG  69
ATOM     69  O   PHE    88       1.188  23.366  50.453  1.00 99.01       1SG  70
ATOM     70  N   ASP    89       2.107  24.819  48.990  1.00 90.33       1SG  71
ATOM     71  CA  ASP    89       2.509  25.751  49.998  1.00 90.33       1SG  72
ATOM     72  CB  ASP    89       3.158  27.007  49.390  1.00 90.33       1SG  73
ATOM     73  CG  ASP    89       3.814  27.802  50.508  1.00 90.33       1SG  74
ATOM     74  OD1 ASP    89       4.455  27.168  51.388  1.00 90.33       1SG  75
ATOM     75  OD2 ASP    89       3.701  29.056  50.486  1.00 90.33       1SG  76
ATOM     76  C   ASP    89       1.343  26.206  50.814  1.00 90.33       1SG  77
ATOM     77  O   ASP    89       1.402  26.163  52.043  1.00 90.33       1SG  78
TER
END
