
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , 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:    61       1_B - 61_B        1.39     1.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.39     1.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      22_B - 56_B        1.00     1.72
  LONGEST_CONTINUOUS_SEGMENT:    35      23_B - 57_B        0.95     1.77
  LCS_AVERAGE:     45.18

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B     15   61   61      8   23   43   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     15   61   61      8   13   39   53   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     15   61   61      8   15   36   51   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     15   61   61      8   20   43   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     15   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     15   61   61     11   27   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     15   61   61      8   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     15   61   61     19   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     15   61   61      8   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     15   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     15   61   61      8   24   38   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     15   61   61      8   13   23   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     15   61   61      8   24   36   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     15   61   61      8   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     15   61   61      8   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     13   61   61      8   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     13   61   61      8   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     13   61   61     10   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     13   61   61      8   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     13   61   61     10   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     11   61   61      3    5    9   26   57   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     35   61   61      3   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     35   61   61     11   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     35   61   61      7   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     35   61   61     10   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     35   61   61      7   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     35   61   61      7   25   45   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     35   61   61      9   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     35   61   61      9   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     35   61   61      9   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     35   61   61      9   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     35   61   61     11   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     35   61   61      9   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     35   61   61     11   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     35   61   61     11   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     35   61   61     11   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     35   61   61     11   27   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     35   61   61      8   27   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     35   61   61      8   27   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     35   61   61      9   27   44   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     35   61   61      9   17   34   53   57   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     35   61   61      5   27   44   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     35   61   61     11   30   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     35   61   61     10   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     35   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     30   61   61     19   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     30   61   61     14   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     30   61   61     19   31   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     30   61   61     19   28   47   54   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  81.73  (  45.18  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     19     31     47     54     58     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  31.15  50.82  77.05  88.52  95.08 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.25   0.71   0.99   1.15   1.27   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39
GDT RMS_ALL_AT   1.89   1.41   1.41   1.41   1.40   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39

# Checking swapping
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     1.961     0    0.388   1.210     6.705   66.071   47.976
LGA    Y     2_B      Y     2_B     2.176     0    0.038   1.355     5.375   66.786   55.000
LGA    I     3_B      I     3_B     2.734     0    0.027   1.286     5.608   62.976   58.631
LGA    R     4_B      R     4_B     1.880     0    0.059   1.220     6.472   75.119   58.788
LGA    E     5_B      E     5_B     0.577     0    0.043   0.835     3.357   90.476   78.624
LGA    L     6_B      L     6_B     1.177     0    0.038   0.905     4.210   88.214   69.524
LGA    R     7_B      R     7_B     0.962     0    0.034   1.027     5.904   90.476   65.281
LGA    A     8_B      A     8_B     1.049     0    0.054   0.054     1.624   81.548   83.333
LGA    A     9_B      A     9_B     1.271     0    0.040   0.043     1.845   81.548   81.524
LGA    L    10_B      L    10_B     0.850     0    0.042   0.108     1.328   85.952   85.952
LGA    I    11_B      I    11_B     1.965     0    0.028   1.301     4.456   69.048   67.619
LGA    L    12_B      L    12_B     2.552     0    0.133   0.938     5.128   62.857   57.202
LGA    L    13_B      L    13_B     2.103     0    0.027   1.463     4.279   70.952   61.607
LGA    A    14_B      A    14_B     1.367     0    0.046   0.052     1.770   83.810   81.619
LGA    L    15_B      L    15_B     0.605     0    0.063   1.027     2.457   95.238   86.429
LGA    K    16_B      K    16_B     0.788     0    0.038   0.842     4.078   90.476   72.804
LGA    K    17_B      K    17_B     0.599     0    0.034   0.836     3.294   90.476   77.407
LGA    Q    18_B      Q    18_B     0.755     0    0.028   1.261     3.090   88.214   74.762
LGA    H    19_B      H    19_B     0.961     0    0.209   0.710     2.286   90.476   80.000
LGA    A    20_B      A    20_B     0.953     0    0.542   0.565     2.129   81.786   81.714
LGA    E    21_B      E    21_B     3.065     0    0.291   0.642     6.435   63.333   41.376
LGA    D    22_B      D    22_B     1.101     0    0.120   0.984     4.785   79.524   66.667
LGA    P    23_B      P    23_B     1.610     0    0.123   0.393     2.024   77.262   81.973
LGA    D    24_B      D    24_B     1.788     0    0.093   1.027     5.008   77.143   60.000
LGA    A    25_B      A    25_B     0.926     0    0.042   0.044     1.476   83.690   86.952
LGA    Q    26_B      Q    26_B     1.640     0    0.026   1.035     4.590   75.000   71.323
LGA    R    27_B      R    27_B     2.046     0    0.030   1.689     6.113   70.833   52.294
LGA    V    28_B      V    28_B     1.519     0    0.021   1.009     2.817   77.143   75.510
LGA    A    29_B      A    29_B     1.442     0    0.035   0.061     1.461   81.429   81.429
LGA    D    30_B      D    30_B     1.351     0    0.043   1.027     5.543   81.548   61.548
LGA    E    31_B      E    31_B     0.902     0    0.033   1.259     5.682   90.595   65.503
LGA    L    32_B      L    32_B     0.918     0    0.045   1.389     3.021   90.476   79.940
LGA    M    33_B      M    33_B     1.091     0    0.038   0.975     4.085   85.952   76.012
LGA    K    34_B      K    34_B     0.536     0    0.040   1.123     6.311   92.857   71.958
LGA    K    35_B      K    35_B     0.346     0    0.075   0.260     1.320   97.619   92.698
LGA    L    36_B      L    36_B     0.806     0    0.028   1.420     3.033   85.952   75.655
LGA    F    37_B      F    37_B     1.640     0    0.048   1.140     3.677   72.976   70.563
LGA    D    38_B      D    38_B     1.774     0    0.042   0.926     3.483   72.976   67.083
LGA    A    39_B      A    39_B     1.494     0    0.020   0.040     1.862   75.000   76.286
LGA    A    40_B      A    40_B     2.088     0    0.112   0.112     2.317   66.786   66.381
LGA    H    41_B      H    41_B     2.841     0    0.098   1.008     7.625   57.262   37.952
LGA    R    42_B      R    42_B     2.172     0    0.154   1.246     5.177   68.810   65.801
LGA    N    43_B      N    43_B     1.181     0    0.052   0.778     3.751   83.810   73.690
LGA    D    44_B      D    44_B     0.781     0    0.094   0.948     4.200   90.476   74.583
LGA    K    45_B      K    45_B     0.401     0    0.091   0.714     7.696   97.619   64.762
LGA    D    46_B      D    46_B     0.514     0    0.042   0.587     2.457   97.619   89.702
LGA    K    47_B      K    47_B     0.257     0    0.026   0.714     4.277  100.000   78.889
LGA    V    48_B      V    48_B     0.131     0    0.072   0.641     1.650  100.000   93.469
LGA    K    49_B      K    49_B     0.559     0    0.052   0.804     2.662   92.857   82.910
LGA    K    50_B      K    50_B     0.650     0    0.043   0.999     4.067   90.476   69.577
LGA    V    51_B      V    51_B     0.458     0    0.030   1.128     2.628   97.619   87.483
LGA    V    52_B      V    52_B     0.324     0    0.033   0.908     2.052   97.619   89.728
LGA    E    53_B      E    53_B     0.580     0    0.026   0.949     4.132   92.857   78.201
LGA    E    54_B      E    54_B     0.872     0    0.038   1.026     4.018   90.476   76.772
LGA    A    55_B      A    55_B     0.793     0    0.039   0.055     0.996   90.476   90.476
LGA    K    56_B      K    56_B     0.645     0    0.047   0.818     3.056   90.476   82.381
LGA    K    57_B      K    57_B     0.918     0    0.031   1.011     3.601   85.952   74.762
LGA    V    58_B      V    58_B     1.393     0    0.076   1.061     3.712   81.429   69.320
LGA    V    59_B      V    59_B     1.252     0    0.074   0.257     1.680   81.429   80.204
LGA    S    60_B      S    60_B     0.949     0    0.194   0.207     2.102   81.786   84.683
LGA    T    61_B      T    61_B     1.431     0    0.038   1.135     3.596   75.119   70.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     1.394          1.375                  2.379           82.865   73.152

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    1.39    84.836    93.277     4.083

LGA_LOCAL      RMSD:   1.394  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.394  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.394  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.954741 * X  +  -0.233355 * Y  +  -0.184434 * Z  +   0.040168
  Y_new =  -0.223361 * X  +  -0.971959 * Y  +   0.073523 * Z  +  -8.912662
  Z_new =  -0.196419 * X  +  -0.029000 * Y  +  -0.980091 * Z  +  39.280357 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.229816  0.197705 -3.112012   [DEG:  -13.1675   11.3276 -178.3051 ]
ZXZ: -1.950132  2.941716 -1.717382   [DEG: -111.7343  168.5479  -98.3987 ]
 
# END of job
