
#######################################################
#                                                     #
#                        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    8 (   59),  selected    8 , name T0298TS268_3_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected    8 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_3_1-D2.T0298_D2.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:     8       130 - 137         2.84     2.84
  LCS_AVERAGE:      4.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       130 - 136         1.96     3.31
  LCS_AVERAGE:      3.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       130 - 134         0.60     3.28
  LCS_AVERAGE:      2.28

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:  186
LCS_GDT     C     130     C     130      5    7    8     4    5    5    5    6    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     131     A     131      5    7    8     4    5    5    5    6    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V     132     V     132      5    7    8     4    5    5    5    6    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     133     A     133      5    7    8     4    5    5    5    6    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     134     A     134      5    7    8     3    5    5    5    6    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     135     E     135      3    7    8     1    3    3    4    6    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     136     L     136      3    7    8     0    3    3    4    5    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     C     137     C     137      3    4    8     0    3    3    4    4    4    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   3.38  (   2.28    3.56    4.30 )

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      7      7      7      8      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.15   2.69   2.69   2.69   3.23   3.76   3.76   3.76   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30
GDT RMS_LOCAL    0.28   0.60   0.60   0.60   1.51   1.96   1.96   1.96   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84
GDT RMS_ALL_CA   3.42   3.28   3.28   3.28   3.65   3.31   3.31   3.31   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130          0.950
LGA    A     131      A     131          1.261
LGA    V     132      V     132          1.955
LGA    A     133      A     133          1.384
LGA    A     134      A     134          1.128
LGA    E     135      E     135          2.836
LGA    L     136      L     136          3.043
LGA    C     137      C     137          7.794

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  186    4.0      7    1.96     3.360     3.593     0.340

LGA_LOCAL      RMSD =  1.957  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.308  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.837  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.652668 * X  +   0.705154 * Y  +   0.277096 * Z  + -37.663784
  Y_new =   0.313933 * X  +   0.584560 * Y  +  -0.748155 * Z  +  72.524963
  Z_new =  -0.689543 * X  +  -0.401307 * Y  +  -0.602895 * Z  +  64.162552 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.554306    0.587287  [ DEG:  -146.3509     33.6491 ]
  Theta =   0.760858    2.380734  [ DEG:    43.5940    136.4060 ]
  Phi   =   2.693260   -0.448332  [ DEG:   154.3125    -25.6875 ]
 
# 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: T0298TS268_3_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_3_1-D2.T0298_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  186   4.0    7   1.96   3.593     2.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1p5f_A
ATOM   1050  N   CYS   130     -10.445  74.456  -1.674  1.00  0.00
ATOM   1051  CA  CYS   130     -10.789  73.115  -1.291  1.00  0.00
ATOM   1052  C   CYS   130     -11.022  73.032   0.185  1.00  0.00
ATOM   1053  O   CYS   130     -11.469  73.985   0.815  1.00  0.00
ATOM   1054  CB  CYS   130      -9.660  72.148  -1.656  1.00  0.00
ATOM   1055  SG  CYS   130      -9.346  72.001  -3.429  1.00  0.00
ATOM   1056  HN  CYS   130      -9.403  74.780  -1.815  1.00  0.00
ATOM   1057  N   ALA   131     -10.725  71.844   0.758  1.00  0.00
ATOM   1058  CA  ALA   131     -10.988  71.517   2.130  1.00  0.00
ATOM   1059  C   ALA   131     -10.251  72.446   3.038  1.00  0.00
ATOM   1060  O   ALA   131     -10.773  72.839   4.081  1.00  0.00
ATOM   1061  CB  ALA   131     -10.543  70.093   2.430  1.00  0.00
ATOM   1062  HN  ALA   131     -10.250  71.118   0.083  1.00  0.00
ATOM   1063  N   VAL   132      -9.011  72.813   2.671  1.00  0.00
ATOM   1064  CA  VAL   132      -8.259  73.698   3.510  1.00  0.00
ATOM   1065  C   VAL   132      -9.074  74.936   3.633  1.00  0.00
ATOM   1066  O   VAL   132      -9.253  75.466   4.727  1.00  0.00
ATOM   1067  CB  VAL   132      -6.884  74.023   2.899  1.00  0.00
ATOM   1068  CG1 VAL   132      -6.189  75.113   3.702  1.00  0.00
ATOM   1069  CG2 VAL   132      -5.996  72.788   2.895  1.00  0.00
ATOM   1070  HN  VAL   132      -8.628  72.406   1.723  1.00  0.00
ATOM   1071  N   ALA   133      -9.621  75.418   2.507  1.00  0.00
ATOM   1072  CA  ALA   133     -10.512  76.530   2.617  1.00  0.00
ATOM   1073  C   ALA   133     -11.740  75.982   3.265  1.00  0.00
ATOM   1074  O   ALA   133     -12.063  74.805   3.140  1.00  0.00
ATOM   1075  CB  ALA   133     -10.824  77.098   1.240  1.00  0.00
ATOM   1076  HN  ALA   133      -9.357  74.934   1.555  1.00  0.00
ATOM   1077  N   ALA   134     -12.459  76.827   4.005  1.00  0.00
ATOM   1078  CA  ALA   134     -13.617  76.357   4.695  1.00  0.00
ATOM   1079  C   ALA   134     -13.969  77.498   5.565  1.00  0.00
ATOM   1080  O   ALA   134     -13.874  78.646   5.140  1.00  0.00
ATOM   1081  CB  ALA   134     -13.287  75.104   5.492  1.00  0.00
ATOM   1082  HN  ALA   134     -12.111  77.870   4.047  1.00  0.00
ATOM   1083  N   GLU   135     -14.455  77.233   6.786  1.00  0.00
ATOM   1084  CA  GLU   135     -14.684  78.387   7.594  1.00  0.00
ATOM   1085  C   GLU   135     -14.158  78.119   8.962  1.00  0.00
ATOM   1086  O   GLU   135     -14.118  76.978   9.415  1.00  0.00
ATOM   1087  CB  GLU   135     -16.180  78.696   7.675  1.00  0.00
ATOM   1088  CG  GLU   135     -16.828  78.989   6.332  1.00  0.00
ATOM   1089  CD  GLU   135     -16.427  80.341   5.776  1.00  0.00
ATOM   1090  OE1 GLU   135     -15.872  81.158   6.541  1.00  0.00
ATOM   1091  OE2 GLU   135     -16.665  80.585   4.575  1.00  0.00
ATOM   1092  HN  GLU   135     -14.644  76.192   7.088  1.00  0.00
ATOM   1093  N   LEU   136     -13.705  79.192   9.641  1.00  0.00
ATOM   1094  CA  LEU   136     -13.253  79.075  10.992  1.00  0.00
ATOM   1095  C   LEU   136     -11.882  78.493  11.012  1.00  0.00
ATOM   1096  O   LEU   136     -11.464  77.799  10.085  1.00  0.00
ATOM   1097  CB  LEU   136     -14.187  78.166  11.794  1.00  0.00
ATOM   1098  CG  LEU   136     -15.650  78.606  11.881  1.00  0.00
ATOM   1099  CD1 LEU   136     -16.474  77.581  12.645  1.00  0.00
ATOM   1100  CD2 LEU   136     -15.768  79.942  12.597  1.00  0.00
ATOM   1101  HN  LEU   136     -13.705  80.149   9.099  1.00  0.00
ATOM   1102  N   CYS   137     -11.131  78.808  12.083  1.00  0.00
ATOM   1103  CA  CYS   137      -9.802  78.296  12.223  1.00  0.00
ATOM   1104  C   CYS   137      -9.785  76.910  11.585  1.00  0.00
ATOM   1105  O   CYS   137      -8.902  76.664  10.717  1.00  0.00
ATOM   1106  CB  CYS   137      -9.416  78.201  13.701  1.00  0.00
ATOM   1107  SG  CYS   137      -9.278  79.796  14.540  1.00  0.00
ATOM   1108  HN  CYS   137     -11.593  79.469  12.831  1.00  0.00
TER
END
