
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   32 (  260),  selected   32 , name one
# Molecule2: number of CA atoms  192 ( 1575),  selected   32 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      69_D - 90_D        4.99     8.86
  LONGEST_CONTINUOUS_SEGMENT:    22      70_D - 91_D        4.59     9.20
  LONGEST_CONTINUOUS_SEGMENT:    22      71_D - 92_D        4.60     9.75
  LONGEST_CONTINUOUS_SEGMENT:    22      75_D - 96_D        4.72    13.94
  LCS_AVERAGE:     10.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      67_D - 74_D        1.91    26.31
  LCS_AVERAGE:      3.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      68_D - 73_D        0.77    26.27
  LCS_AVERAGE:      2.43

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   32
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     N    65_D     N    65_D      4    5   12      3    4    4    4    5    5    5    5    6    8   11   11   11   11   16   16   16   22   25   27 
LCS_GDT     L    66_D     L    66_D      4    5   13      3    4    4    4    5    5    5    8    8    9   13   15   17   21   21   24   26   26   27   27 
LCS_GDT     M    67_D     M    67_D      4    8   13      3    4    4    4    6    7    7    8    8    9   11   15   17   21   21   24   26   26   27   27 
LCS_GDT     A    68_D     A    68_D      6    8   20      3    5    6    7    7    7    8    9   12   14   15   17   18   21   21   24   26   26   27   27 
LCS_GDT     F    69_D     F    69_D      6    8   22      3    5    6    7    7    8   10   10   13   14   16   17   18   21   21   24   26   26   27   27 
LCS_GDT     K    70_D     K    70_D      6    8   22      4    5    6    7    8    9   11   12   13   14   16   17   19   21   22   24   26   26   27   27 
LCS_GDT     P    71_D     P    71_D      6    8   22      4    5    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     I    72_D     I    72_D      6    8   22      4    5    6    7    7    8    9   11   13   15   18   21   21   21   22   24   26   26   27   27 
LCS_GDT     G    73_D     G    73_D      6    8   22      4    5    6    7    7    7    9   10   13   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     P    74_D     P    74_D      5    8   22      3    4    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     L    75_D     L    75_D      5    6   22      3    4    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     V    76_D     V    76_D      5    6   22      3    4    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     G    77_D     G    77_D      5    6   22      3    4    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     N    78_D     N    78_D      5    6   22      4    5    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     E    79_D     E    79_D      5    6   22      4    5    5    6    7    9   11   13   15   17   19   21   21   21   22   23   26   26   27   27 
LCS_GDT     E    80_D     E    80_D      5    6   22      4    5    5    5    7    8   10   12   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     E    81_D     E    81_D      5    6   22      4    5    5    5    7    8    9   12   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     W    82_D     W    82_D      5    7   22      3    5    7    7    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     N    83_D     N    83_D      3    7   22      3    3    4    5    6   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     Y    84_D     Y    84_D      4    7   22      4    4    4    6    7    9   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     N    85_D     N    85_D      4    7   22      4    4    4    6    8   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     S    86_D     S    86_D      4    7   22      4    4    4    6    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     D    87_D     D    87_D      4    7   22      4    4    4    6    9   10   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     D    88_D     D    88_D      3    7   22      3    3    4    6    6    9   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     S    89_D     S    89_D      3    5   22      0    3    4    4    6    9   11   13   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     F    90_D     F    90_D      3    5   22      1    3    4    4    7    8    9   11   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     Q    91_D     Q    91_D      3    3   22      1    3    3    4    7    8   11   12   15   17   19   21   21   21   22   24   26   26   27   27 
LCS_GDT     N    92_D     N    92_D      5    5   22      4    5    5    5    7    7    9   12   13   17   19   19   20   21   21   23   23   26   27   27 
LCS_GDT     N    93_D     N    93_D      5    5   22      4    5    5    5    5    5    6   10   11   13   14   17   20   21   21   21   22   22   24   26 
LCS_GDT     R    94_D     R    94_D      5    5   22      4    5    5    5    5    7    9   12   13   16   19   19   20   21   21   23   23   23   25   26 
LCS_GDT     L    95_D     L    95_D      5    5   22      4    5    5    5    5    5    8   12   13   17   19   19   20   21   21   23   23   23   25   26 
LCS_GDT     S    96_D     S    96_D      5    5   22      3    5    5    5    5    5    8   12   13   17   19   19   20   21   21   23   23   23   25   26 
LCS_AVERAGE  LCS_A:   5.57  (   2.43    3.30   10.97 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT      4      5      7      7      9     10     11     13     15     17     19     21     21     21     22     24     26     26     27     27 
GDT PERCENT_AT   2.08   2.60   3.65   3.65   4.69   5.21   5.73   6.77   7.81   8.85   9.90  10.94  10.94  10.94  11.46  12.50  13.54  13.54  14.06  14.06
GDT RMS_LOCAL    0.21   0.49   1.14   1.04   1.83   2.03   2.19   2.64   3.24   3.61   3.85   4.15   4.15   4.15   4.59   5.62   5.89   5.89   6.16   6.16
GDT RMS_ALL_AT  26.52  26.56   9.19  25.94   9.02   9.12   9.21   9.58   9.56  10.22   9.75   9.72   9.72   9.72   9.20   8.15   8.21   8.21   8.10   8.10

# Checking swapping
#   possible swapping detected:  F    69_D      F    69_D
#   possible swapping detected:  E    80_D      E    80_D
#   possible swapping detected:  E    81_D      E    81_D
#   possible swapping detected:  Y    84_D      Y    84_D
#   possible swapping detected:  D    88_D      D    88_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    65_D      N    65_D    19.083     0    0.074   0.420    22.745    0.000    0.000
LGA    L    66_D      L    66_D    15.061     0    0.139   0.132    17.530    0.000    0.000
LGA    M    67_D      M    67_D    14.715     0    0.086   0.626    19.202    0.000    0.000
LGA    A    68_D      A    68_D    14.838     0    0.559   0.535    17.009    0.000    0.000
LGA    F    69_D      F    69_D    10.587     0    0.141   1.229    16.516    0.476    0.173
LGA    K    70_D      K    70_D     7.280     0    0.097   0.216    18.100   19.405    8.783
LGA    P    71_D      P    71_D     1.414     0    0.025   0.260     5.105   52.024   52.313
LGA    I    72_D      I    72_D     8.395     0    0.138   1.258    13.159    7.262    3.631
LGA    G    73_D      G    73_D     8.301     0    0.642   0.642     8.301   13.095   13.095
LGA    P    74_D      P    74_D     2.747     0    0.692   0.795     6.010   56.548   44.694
LGA    L    75_D      L    75_D     2.509     0    0.045   0.107     5.674   59.048   46.905
LGA    V    76_D      V    76_D     2.086     0    0.634   1.438     4.665   61.429   60.680
LGA    G    77_D      G    77_D     2.221     0    0.247   0.247     2.385   64.762   64.762
LGA    N    78_D      N    78_D     2.337     0    0.578   1.235     6.670   70.952   49.702
LGA    E    79_D      E    79_D     3.904     0    0.013   1.202    11.951   46.786   23.069
LGA    E    80_D      E    80_D     6.439     0    0.200   1.059    12.958   22.738   10.423
LGA    E    81_D      E    81_D     5.669     0    0.297   0.834    11.804   26.429   13.280
LGA    W    82_D      W    82_D     3.091     0    0.605   1.366    12.288   65.357   23.980
LGA    N    83_D      N    83_D     2.776     0    0.609   0.680     6.635   55.595   40.655
LGA    Y    84_D      Y    84_D     4.087     0    0.472   0.461    11.024   45.119   19.762
LGA    N    85_D      N    85_D     2.186     0    0.036   0.169     3.609   70.952   64.286
LGA    S    86_D      S    86_D     1.262     0    0.213   0.707     1.880   81.548   80.079
LGA    D    87_D      D    87_D     2.173     0    0.597   0.875     5.966   61.190   47.024
LGA    D    88_D      D    88_D     5.901     0    0.176   1.002    11.204   25.119   12.917
LGA    S    89_D      S    89_D     7.910     0    0.607   0.788    10.159    8.333    5.794
LGA    F    90_D      F    90_D     6.340     0    0.611   1.496     8.230   16.190   15.281
LGA    Q    91_D      Q    91_D     8.045     0    0.592   1.436     9.948    4.405    3.492
LGA    N    92_D      N    92_D    12.910     0    0.607   0.997    15.820    0.000    0.000
LGA    N    93_D      N    93_D    16.960     0    0.079   0.155    18.823    0.000    0.000
LGA    R    94_D      R    94_D    15.436     0    0.061   0.647    15.679    0.000    0.000
LGA    L    95_D      L    95_D    14.844     0    0.588   0.482    17.320    0.000    0.000
LGA    S    96_D      S    96_D    18.101     0    0.687   0.937    21.871    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       32     128    128  100.00     260    260  100.00               192
SUMMARY(RMSD_GDC):     7.862          7.735                  9.212            4.869    3.671

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   32  192    4.0     13    2.64     6.380     5.863     0.474

LGA_LOCAL      RMSD:   2.644  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.584  Number of assigned atoms:   32 
Std_ASGN_ATOMS RMSD:   7.862  Standard rmsd on all 32 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.925558 * X  +  -0.083910 * Y  +   0.369191 * Z  + -103.712135
  Y_new =  -0.353381 * X  +   0.158517 * Y  +   0.921951 * Z  + -123.189240
  Z_new =  -0.135884 * X  +  -0.983784 * Y  +   0.117064 * Z  + -31.229103 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.364722  0.136306 -1.452359   [DEG:  -20.8970    7.8097  -83.2141 ]
ZXZ:  2.760703  1.453463 -3.004337   [DEG:  158.1766   83.2773 -172.1358 ]
 
# END of job
