
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.56     1.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.56     1.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        0.90     1.62
  LONGEST_CONTINUOUS_SEGMENT:    37       3_B - 39_B        0.94     1.59
  LCS_AVERAGE:     85.72

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B     37   41   41      3   11   20   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S     3_B     S     3_B     37   41   41      4   24   30   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B     37   41   41      6   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     37   41   41      7   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     37   41   41      5   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     37   41   41     15   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     37   41   41     15   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     37   41   41     15   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     37   41   41     11   29   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     37   41   41     11   29   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     37   41   41     10   16   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     37   41   41     11   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     37   41   41     11   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     37   41   41     16   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     37   41   41     11   30   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     37   41   41     11   29   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     37   41   41     10   28   35   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     37   41   41      4   12   19   36   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     16   41   41      4    5   12   16   23   37   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     16   41   41      4   10   15   24   37   39   39   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   41   41      3    3    3    3    4    4   31   36   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  95.24  (  85.72  100.00  100.00 )

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     16     30     35     36     37     39     39     40     40     41     41     41     41     41     41     41     41     41     41     41 
GDT PERCENT_AT  39.02  73.17  85.37  87.80  90.24  95.12  95.12  97.56  97.56 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.60   0.75   0.83   0.90   1.13   1.13   1.33   1.33   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56
GDT RMS_ALL_AT   1.66   1.60   1.63   1.61   1.62   1.57   1.57   1.58   1.58   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56

# Checking swapping
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    32_B      E    32_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     2.675     0    0.334   0.452     4.586   45.714   51.143
LGA    S     3_B      S     3_B     2.300     0    0.147   0.518     2.423   68.810   67.460
LGA    Q     4_B      Q     4_B     1.305     0    0.005   0.645     2.934   79.286   73.968
LGA    R     5_B      R     5_B     0.767     0    0.096   1.194     4.532   88.214   71.472
LGA    L     6_B      L     6_B     0.639     0    0.072   0.109     1.548   88.214   84.881
LGA    F     7_B      F     7_B     0.479     0    0.032   0.091     0.755   92.857   95.671
LGA    V     8_B      V     8_B     0.878     0    0.046   1.148     2.549   90.476   81.905
LGA    L     9_B      L     9_B     0.418     0    0.022   0.130     0.695   92.857   91.667
LGA    D    10_B      D    10_B     0.343     0    0.039   0.489     1.531  100.000   93.095
LGA    N    11_B      N    11_B     0.305     0    0.071   0.872     2.195   95.238   87.440
LGA    E    12_B      E    12_B     0.774     0    0.045   1.213     6.215   90.476   63.386
LGA    R    13_B      R    13_B     0.761     0    0.046   1.142     3.574   90.476   76.926
LGA    Y    14_B      Y    14_B     0.172     0    0.051   0.116     0.736  100.000   98.413
LGA    D    15_B      D    15_B     0.194     0    0.026   0.447     1.423  100.000   94.167
LGA    S    16_B      S    16_B     0.378     0    0.030   0.792     2.555  100.000   92.857
LGA    F    17_B      F    17_B     0.227     0    0.025   0.209     0.778  100.000   95.671
LGA    I    18_B      I    18_B     0.152     0    0.030   0.114     0.471  100.000  100.000
LGA    T    19_B      T    19_B     0.204     0    0.015   0.224     0.915  100.000   98.639
LGA    Q    20_B      Q    20_B     0.489     0    0.029   0.801     2.293   97.619   88.889
LGA    L    21_B      L    21_B     0.846     0    0.019   1.309     3.262   90.476   83.214
LGA    E    22_B      E    22_B     0.787     0    0.029   0.742     2.120   90.476   81.746
LGA    A    23_B      A    23_B     0.152     0    0.081   0.097     0.327  100.000  100.000
LGA    P    24_B      P    24_B     0.612     0    0.040   0.048     0.662   92.857   93.197
LGA    V    25_B      V    25_B     0.879     0    0.095   1.180     3.032   85.952   79.592
LGA    Q    26_B      Q    26_B     1.407     0    0.026   1.166     5.998   81.429   61.270
LGA    N    27_B      N    27_B     1.388     0    0.068   0.078     1.449   81.429   81.429
LGA    A    28_B      A    28_B     1.526     0    0.111   0.122     1.818   81.548   79.810
LGA    E    29_B      E    29_B     0.986     0    0.054   0.761     2.348   88.214   83.598
LGA    G    30_B      G    30_B     0.561     0    0.090   0.090     0.637   92.857   92.857
LGA    R    31_B      R    31_B     0.750     0    0.041   1.075     5.422   90.476   73.636
LGA    E    32_B      E    32_B     0.755     0    0.103   0.779     4.098   90.476   76.349
LGA    R    33_B      R    33_B     0.595     0    0.038   1.246     3.788   90.476   81.429
LGA    L    34_B      L    34_B     0.559     0    0.019   0.070     0.965   90.476   90.476
LGA    M    35_B      M    35_B     0.702     0    0.040   0.605     2.556   90.476   86.310
LGA    A    36_B      A    36_B     0.995     0    0.014   0.027     1.349   85.952   86.857
LGA    V    37_B      V    37_B     1.070     0    0.053   0.078     1.206   83.690   82.721
LGA    K    38_B      K    38_B     1.532     4    0.118   0.140     3.218   69.286   37.143
LGA    P    39_B      P    39_B     2.418     0    0.124   0.158     2.733   67.024   69.728
LGA    E    40_B      E    40_B     4.402     0    0.320   0.871     7.496   41.786   25.714
LGA    W    41_B      W    41_B     3.186     0    0.554   1.303     8.253   43.690   35.918
LGA    K    42_B      K    42_B     5.645     0    0.173   0.984    12.143   26.310   12.328

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     1.561          1.585                  2.428           84.771   78.121

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     40    1.33    89.634    94.469     2.803

LGA_LOCAL      RMSD:   1.327  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.580  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   1.561  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.174312 * X  +  -0.113277 * Y  +   0.978153 * Z  +  19.658899
  Y_new =   0.862484 * X  +   0.461738 * Y  +   0.207171 * Z  +  -8.406803
  Z_new =  -0.475118 * X  +   0.879754 * Y  +   0.017214 * Z  +  34.599243 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.770214  0.495098  1.551232   [DEG:  101.4258   28.3670   88.8791 ]
ZXZ:  1.779510  1.553582 -0.495178   [DEG:  101.9584   89.0137  -28.3716 ]
 
# END of job
