
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS249_5_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_5_2-D1.T0372_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       290 - 298         3.83     3.83
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       290 - 294         1.90     5.26
  LONGEST_CONTINUOUS_SEGMENT:     5       292 - 296         1.90     5.96
  LCS_AVERAGE:      3.79

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.66     6.82
  LCS_AVERAGE:      2.73

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:  126
LCS_GDT     K     290     K     290      4    5    9     0    4    4    4    5    5    5    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      4    5    9     3    4    4    4    5    5    5    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      4    5    9     3    4    4    4    5    5    6    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    5    9     3    4    4    4    5    5    6    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      3    5    9     3    3    3    4    5    5    6    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      3    5    9     3    3    3    4    5    5    6    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      3    5    9     3    3    3    4    5    5    6    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      3    4    9     3    3    3    4    4    4    5    5    5    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    4    9     3    3    3    4    4    5    6    6    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.56  (   2.73    3.79    7.14 )

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      4      4      4      5      5      6      6      8      8      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.17   3.17   3.97   3.97   4.76   4.76   6.35   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.08   0.66   0.66   0.66   1.90   1.90   2.37   2.37   3.38   3.38   3.83   3.83   3.83   3.83   3.83   3.83   3.83   3.83   3.83   3.83
GDT RMS_ALL_CA   7.75   6.82   6.82   6.82   5.96   5.96   4.84   4.84   3.96   3.96   3.83   3.83   3.83   3.83   3.83   3.83   3.83   3.83   3.83   3.83

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          5.779
LGA    Y     291      Y     291          4.876
LGA    M     292      M     292          2.655
LGA    A     293      A     293          2.363
LGA    C     294      C     294          1.192
LGA    L     295      L     295          3.690
LGA    K     296      K     296          2.820
LGA    D     297      D     297          7.102
LGA    H     298      H     298          2.991

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    2.37     4.563     4.680     0.243

LGA_LOCAL      RMSD =  2.372  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.112  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  3.827  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.090578 * X  +  -0.019862 * Y  +   0.995691 * Z  +  26.554613
  Y_new =   0.467588 * X  +   0.881899 * Y  +   0.060128 * Z  +  52.610535
  Z_new =  -0.879294 * X  +   0.471019 * Y  +  -0.070593 * Z  +  -3.685863 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.719562   -1.422031  [ DEG:    98.5237    -81.4763 ]
  Theta =   1.074377    2.067215  [ DEG:    61.5573    118.4427 ]
  Phi   =   1.762139   -1.379454  [ DEG:   100.9631    -79.0369 ]
 
# 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: T0372TS249_5_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_5_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  126   4.0    6   2.37   4.680     3.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      22.469  44.796   1.602  1.00  0.00
ATOM   1036  CA  LYS   290      23.755  44.718   2.224  1.00  0.00
ATOM   1037  C   LYS   290      24.742  45.016   1.171  1.00  0.00
ATOM   1038  O   LYS   290      25.906  45.283   1.476  1.00  0.00
ATOM   1039  CB  LYS   290      24.106  43.330   2.776  1.00  0.00
ATOM   1040  CG  LYS   290      23.328  42.961   4.035  1.00  0.00
ATOM   1041  CD  LYS   290      23.490  41.496   4.429  1.00  0.00
ATOM   1042  CE  LYS   290      22.886  41.169   5.795  1.00  0.00
ATOM   1043  NZ  LYS   290      23.586  41.933   6.852  1.00  0.00
ATOM   1044  N   TYR   291      24.314  44.864  -0.098  1.00  0.00
ATOM   1045  CA  TYR   291      25.189  45.242  -1.151  1.00  0.00
ATOM   1046  C   TYR   291      25.439  46.646  -0.809  1.00  0.00
ATOM   1047  O   TYR   291      24.526  47.387  -0.444  1.00  0.00
ATOM   1048  CB  TYR   291      24.550  45.213  -2.544  1.00  0.00
ATOM   1049  CG  TYR   291      23.865  43.899  -2.628  1.00  0.00
ATOM   1050  CD1 TYR   291      24.561  42.714  -2.613  1.00  0.00
ATOM   1051  CD2 TYR   291      22.498  43.873  -2.742  1.00  0.00
ATOM   1052  CE1 TYR   291      23.889  41.516  -2.688  1.00  0.00
ATOM   1053  CE2 TYR   291      21.819  42.684  -2.818  1.00  0.00
ATOM   1054  CZ  TYR   291      22.518  41.503  -2.786  1.00  0.00
ATOM   1055  OH  TYR   291      21.828  40.275  -2.861  1.00  0.00
ATOM   1056  N   MET   292      26.707  47.034  -0.812  1.00  0.00
ATOM   1057  CA  MET   292      26.882  48.400  -0.515  1.00  0.00
ATOM   1058  C   MET   292      26.458  49.015  -1.790  1.00  0.00
ATOM   1059  O   MET   292      25.318  48.959  -2.249  1.00  0.00
ATOM   1060  CB  MET   292      28.355  48.796  -0.301  1.00  0.00
ATOM   1061  CG  MET   292      29.020  48.057   0.859  1.00  0.00
ATOM   1062  SD  MET   292      28.396  48.491   2.508  1.00  0.00
ATOM   1063  CE  MET   292      29.473  49.942   2.695  1.00  0.00
ATOM   1064  N   ALA   293      27.397  49.736  -2.345  1.00  0.00
ATOM   1065  CA  ALA   293      27.252  50.327  -3.613  1.00  0.00
ATOM   1066  C   ALA   293      27.424  49.357  -4.741  1.00  0.00
ATOM   1067  O   ALA   293      27.065  49.678  -5.869  1.00  0.00
ATOM   1068  CB  ALA   293      28.113  51.580  -3.720  1.00  0.00
ATOM   1069  N   CYS   294      27.988  48.155  -4.488  1.00  0.00
ATOM   1070  CA  CYS   294      28.521  47.338  -5.544  1.00  0.00
ATOM   1071  C   CYS   294      27.644  47.157  -6.731  1.00  0.00
ATOM   1072  O   CYS   294      28.024  47.619  -7.807  1.00  0.00
ATOM   1073  CB  CYS   294      28.951  45.952  -5.042  1.00  0.00
ATOM   1074  SG  CYS   294      27.658  45.140  -4.063  1.00  0.00
ATOM   1075  N   LEU   295      26.448  46.566  -6.591  1.00  0.00
ATOM   1076  CA  LEU   295      25.753  46.262  -7.805  1.00  0.00
ATOM   1077  C   LEU   295      25.415  47.504  -8.528  1.00  0.00
ATOM   1078  O   LEU   295      25.793  47.721  -9.680  1.00  0.00
ATOM   1079  CB  LEU   295      24.431  45.519  -7.573  1.00  0.00
ATOM   1080  CG  LEU   295      24.601  44.178  -6.841  1.00  0.00
ATOM   1081  CD1 LEU   295      24.978  44.390  -5.367  1.00  0.00
ATOM   1082  CD2 LEU   295      23.370  43.284  -7.022  1.00  0.00
ATOM   1083  N   LYS   296      24.768  48.411  -7.814  1.00  0.00
ATOM   1084  CA  LYS   296      24.229  49.457  -8.586  1.00  0.00
ATOM   1085  C   LYS   296      25.207  50.468  -9.048  1.00  0.00
ATOM   1086  O   LYS   296      24.870  51.195  -9.963  1.00  0.00
ATOM   1087  CB  LYS   296      23.021  50.149  -7.965  1.00  0.00
ATOM   1088  CG  LYS   296      22.093  50.614  -9.082  1.00  0.00
ATOM   1089  CD  LYS   296      21.463  49.426  -9.825  1.00  0.00
ATOM   1090  CE  LYS   296      22.114  49.052 -11.163  1.00  0.00
ATOM   1091  NZ  LYS   296      23.264  48.133 -10.979  1.00  0.00
ATOM   1092  N   ASP   297      26.378  50.632  -8.403  1.00  0.00
ATOM   1093  CA  ASP   297      27.268  51.731  -8.714  1.00  0.00
ATOM   1094  C   ASP   297      27.663  51.613 -10.090  1.00  0.00
ATOM   1095  O   ASP   297      28.002  52.576 -10.772  1.00  0.00
ATOM   1096  CB  ASP   297      28.666  51.595  -8.134  1.00  0.00
ATOM   1097  CG  ASP   297      28.584  51.814  -6.676  1.00  0.00
ATOM   1098  OD1 ASP   297      27.561  52.408  -6.241  1.00  0.00
ATOM   1099  OD2 ASP   297      29.574  51.428  -5.998  1.00  0.00
ATOM   1100  N   HIS   298      27.737  50.363 -10.477  1.00  0.00
ATOM   1101  CA  HIS   298      28.162  50.094 -11.774  1.00  0.00
ATOM   1102  C   HIS   298      27.135  50.619 -12.731  1.00  0.00
ATOM   1103  O   HIS   298      27.585  51.086 -13.772  1.00  0.00
ATOM   1104  CB  HIS   298      28.340  48.578 -11.971  1.00  0.00
ATOM   1105  CG  HIS   298      28.949  48.125 -13.264  1.00  0.00
ATOM   1106  ND1 HIS   298      28.440  47.095 -14.024  1.00  0.00
ATOM   1107  CD2 HIS   298      30.067  48.545 -13.915  1.00  0.00
ATOM   1108  CE1 HIS   298      29.276  46.939 -15.079  1.00  0.00
ATOM   1109  NE2 HIS   298      30.277  47.798 -15.058  1.00  0.00
TER
END
