
#######################################################
#                                                     #
#                        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   31 (  244),  selected   31 , name one
# Molecule2: number of CA atoms   83 (  623),  selected   31 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:E  -ch2:E  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      27_E - 57_E        2.64     2.64
  LCS_AVERAGE:     37.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      33_E - 57_E        1.96     3.01
  LCS_AVERAGE:     28.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      40_E - 57_E        0.92     3.64
  LCS_AVERAGE:     20.68

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   31
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     Q    27_E     Q    27_E     16   18   31     13   15   15   16   16   23   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    28_E     L    28_E     16   18   31     13   15   15   16   16   17   25   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     E    29_E     E    29_E     16   18   31     13   15   15   16   16   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    30_E     L    30_E     16   18   31     13   15   15   16   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     I    31_E     I    31_E     16   18   31     13   15   15   16   16   17   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K    32_E     K    32_E     16   18   31     13   15   15   16   16   17   25   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     Q    33_E     Q    33_E     16   25   31     13   15   15   16   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     F    34_E     F    34_E     16   25   31     13   15   15   16   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     M    35_E     M    35_E     16   25   31     13   15   15   16   16   23   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     A    36_E     A    36_E     16   25   31     13   15   15   16   16   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     E    37_E     E    37_E     16   25   31     13   15   15   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     A    38_E     A    38_E     16   25   31     13   15   15   16   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     M    39_E     M    39_E     16   25   31     13   15   15   16   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K    40_E     K    40_E     18   25   31      4   15   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     I    41_E     I    41_E     18   25   31      4   15   15   16   19   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     G    42_E     G    42_E     18   25   31     10   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     N    43_E     N    43_E     18   25   31     12   16   17   18   19   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K    44_E     K    44_E     18   25   31      3   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     E    45_E     E    45_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     G    46_E     G    46_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    47_E     L    47_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    48_E     L    48_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    49_E     L    49_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    50_E     L    50_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     A    51_E     A    51_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     E    52_E     E    52_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     R    53_E     R    53_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    54_E     L    54_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     E    55_E     E    55_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     A    56_E     A    56_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L    57_E     L    57_E     18   25   31     13   16   17   18   21   25   28   30   31   31   31   31   31   31   31   31   31   31   31   31 
LCS_AVERAGE  LCS_A:  28.84  (  20.68   28.49   37.35 )

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     13     16     17     18     21     25     28     30     31     31     31     31     31     31     31     31     31     31     31     31 
GDT PERCENT_AT  15.66  19.28  20.48  21.69  25.30  30.12  33.73  36.14  37.35  37.35  37.35  37.35  37.35  37.35  37.35  37.35  37.35  37.35  37.35  37.35
GDT RMS_LOCAL    0.25   0.47   0.61   0.91   1.69   1.92   2.30   2.51   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64
GDT RMS_ALL_AT   6.78   3.59   3.72   3.51   2.91   2.93   2.70   2.65   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64

# Checking swapping
#   possible swapping detected:  F    34_E      F    34_E
#   possible swapping detected:  E    52_E      E    52_E
#   possible swapping detected:  E    55_E      E    55_E

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    27_E      Q    27_E     3.907     0    0.030   1.329     9.142   41.905   25.767
LGA    L    28_E      L    28_E     5.309     0    0.067   1.388    10.270   30.119   19.464
LGA    E    29_E      E    29_E     3.657     0    0.024   0.160     4.882   48.690   43.704
LGA    L    30_E      L    30_E     1.907     0    0.103   0.207     2.426   68.810   74.048
LGA    I    31_E      I    31_E     4.208     0    0.009   0.672     8.236   40.357   28.869
LGA    K    32_E      K    32_E     4.494     0    0.016   0.765     9.960   40.238   24.392
LGA    Q    33_E      Q    33_E     2.294     0    0.011   0.827     3.853   66.905   61.640
LGA    F    34_E      F    34_E     2.235     0    0.053   1.168     8.365   66.786   39.307
LGA    M    35_E      M    35_E     3.282     0    0.054   0.731     4.520   51.786   46.131
LGA    A    36_E      A    36_E     3.009     0    0.028   0.028     3.379   57.262   55.810
LGA    E    37_E      E    37_E     1.748     0    0.011   0.925     2.438   72.857   76.825
LGA    A    38_E      A    38_E     2.334     0    0.116   0.124     2.999   64.881   63.333
LGA    M    39_E      M    39_E     2.530     0    0.169   1.257     3.789   64.881   61.310
LGA    K    40_E      K    40_E     1.919     0    0.178   0.692     4.176   67.262   57.037
LGA    I    41_E      I    41_E     3.118     0    0.583   1.047     6.273   52.262   45.476
LGA    G    42_E      G    42_E     1.338     0    0.124   0.124     1.892   75.000   75.000
LGA    N    43_E      N    43_E     2.963     0    0.233   0.908     6.538   59.048   45.952
LGA    K    44_E      K    44_E     2.656     0    0.070   0.614     3.584   62.976   58.360
LGA    E    45_E      E    45_E     2.321     0    0.026   0.169     4.136   66.786   54.656
LGA    G    46_E      G    46_E     2.406     0    0.010   0.010     2.406   64.762   64.762
LGA    L    47_E      L    47_E     1.787     0    0.032   1.378     3.853   70.833   64.226
LGA    L    48_E      L    48_E     1.483     0    0.043   0.109     1.828   75.000   77.202
LGA    L    49_E      L    49_E     1.910     0    0.000   1.395     5.656   72.857   55.060
LGA    L    50_E      L    50_E     1.879     0    0.000   0.025     2.184   72.857   70.833
LGA    A    51_E      A    51_E     1.551     0    0.040   0.045     1.663   77.143   76.286
LGA    E    52_E      E    52_E     1.393     0    0.013   1.109     3.719   79.286   69.947
LGA    R    53_E      R    53_E     1.911     0    0.072   1.470     4.344   72.857   65.238
LGA    L    54_E      L    54_E     1.812     0    0.036   0.032     1.966   72.857   72.857
LGA    E    55_E      E    55_E     1.425     0    0.074   0.641     2.301   75.000   73.862
LGA    A    56_E      A    56_E     1.889     0    0.124   0.128     2.556   66.905   68.095
LGA    L    57_E      L    57_E     1.670     0    0.167   0.178     1.670   72.857   72.857

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       31     124    124  100.00     244    244  100.00                83
SUMMARY(RMSD_GDC):     2.639          2.546                  3.363           23.759   21.546

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   31   83    4.0     30    2.51    28.614    29.845     1.148

LGA_LOCAL      RMSD:   2.514  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.651  Number of assigned atoms:   31 
Std_ASGN_ATOMS RMSD:   2.639  Standard rmsd on all 31 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.209464 * X  +   0.917833 * Y  +  -0.337205 * Z  + -70.698425
  Y_new =  -0.941827 * X  +   0.096679 * Y  +  -0.321893 * Z  + -28.646185
  Z_new =  -0.262843 * X  +   0.385014 * Y  +   0.884691 * Z  + -105.776352 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.351956  0.265968  0.410475   [DEG:  -77.4614   15.2388   23.5185 ]
ZXZ: -0.808627  0.484966 -0.599010   [DEG:  -46.3309   27.7865  -34.3208 ]
 
# END of job
