
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.89     2.75
  LCS_AVERAGE:     46.11

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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_A     D     1_A     20   60   60      0    3    5   51   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   60   60      3   29   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   60   60      5   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   60   60      7   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     20   60   60     11   24   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   60   60     11   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   60   60     11   29   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   60   60     11   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   60   60     11   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   60   60     11   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   60   60     11   24   44   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   60   60     11   26   43   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     20   60   60      3    4   44   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     19   60   60      3    4    4    8   35   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      4   60   60      3    4    6   14   25   31   47   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      4   60   60      5   20   37   44   53   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      4   60   60      3    3    4    6    6    8   16   34   57   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      4   60   60      3    3    4    6   21   47   53   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     35   60   60      6   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   60   60     16   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   60   60      5   30   40   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   60   60     20   30   35   51   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   60   60     20   30   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   60   60     20   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   60   60     18   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   60   60     13   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   60   60     18   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   60   60     14   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   60   60     18   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   60   60      5   25   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   60   60      5   29   45   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   60   60     16   31   46   52   54   55   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     35   60   60      0    3    3   16   35   53   57   59   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  82.04  (  46.11  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     20     31     46     52     54     55     57     59     59     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  33.33  51.67  76.67  86.67  90.00  91.67  95.00  98.33  98.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.68   0.94   1.10   1.17   1.27   1.44   1.70   1.70   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88
GDT RMS_ALL_AT   2.77   1.93   2.11   2.02   2.03   1.97   1.93   1.89   1.89   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88

# Checking swapping
#   possible swapping detected:  D     8_A      D     8_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    42_A      E    42_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     2.751     0    0.097   1.116     6.119   56.071   41.012
LGA    D     2_A      D     2_A     1.121     0    0.459   1.297     7.224   86.071   55.357
LGA    K     3_A      K     3_A     0.981     0    0.055   1.083     8.043   92.857   59.471
LGA    A     4_A      A     4_A     0.772     0    0.030   0.037     1.058   90.476   88.667
LGA    A     5_A      A     5_A     0.974     0    0.059   0.057     1.369   85.952   85.048
LGA    C     6_A      C     6_A     1.321     0    0.047   0.161     2.310   83.690   78.730
LGA    A     7_A      A     7_A     0.580     0    0.036   0.041     0.813   95.238   94.286
LGA    D     8_A      D     8_A     0.693     0    0.029   0.952     3.178   90.476   77.917
LGA    G     9_A      G     9_A     1.089     0    0.046   0.046     1.106   83.690   83.690
LGA    I    10_A      I    10_A     0.855     0    0.040   1.070     2.408   95.238   82.083
LGA    A    11_A      A    11_A     0.292     0    0.033   0.043     0.648   97.619   98.095
LGA    A    12_A      A    12_A     1.015     0    0.032   0.042     1.295   85.952   85.048
LGA    V    13_A      V    13_A     0.764     0    0.046   0.997     2.481   95.238   85.850
LGA    K    14_A      K    14_A     0.192     0    0.034   0.267     0.834   97.619   94.709
LGA    A    15_A      A    15_A     0.954     0    0.070   0.071     1.534   83.810   83.333
LGA    R    16_A      R    16_A     1.053     0    0.031   1.146     8.228   88.214   52.208
LGA    V    17_A      V    17_A     0.355     0    0.039   1.215     3.068   95.238   85.102
LGA    E    18_A      E    18_A     1.436     0    0.425   1.155     6.150   79.286   59.577
LGA    K    19_A      K    19_A     1.863     0    0.571   1.210     3.686   65.476   62.804
LGA    L    20_A      L    20_A     1.535     0    0.153   0.695     7.464   71.429   47.202
LGA    A    21_A      A    21_A     3.510     0    0.092   0.136     5.551   65.595   56.762
LGA    P    22_A      P    22_A     5.073     0    0.083   0.127     8.749   37.500   24.762
LGA    E    23_A      E    23_A     2.783     0    0.488   0.882     7.164   46.786   33.598
LGA    A    24_A      A    24_A     6.561     0    0.229   0.232     8.997   19.524   16.190
LGA    V    25_A      V    25_A     4.687     0    0.598   0.623     8.751   42.738   29.184
LGA    P    26_A      P    26_A     2.457     0    0.661   0.679     4.725   73.571   61.973
LGA    Q    27_A      Q    27_A     2.372     0    0.060   1.264     6.904   64.762   49.788
LGA    K    28_A      K    28_A     1.996     0    0.051   0.516     4.357   70.833   59.153
LGA    L    29_A      L    29_A     0.947     0    0.030   0.996     3.443   85.952   76.786
LGA    K    30_A      K    30_A     1.872     0    0.042   0.267     2.399   72.857   69.259
LGA    R    31_A      R    31_A     2.368     0    0.028   1.321     7.610   68.810   48.225
LGA    A    32_A      A    32_A     1.319     0    0.045   0.046     1.634   81.548   81.524
LGA    L    33_A      L    33_A     0.940     0    0.021   0.853     3.394   85.952   75.595
LGA    K    34_A      K    34_A     1.747     0    0.052   0.874     6.334   75.000   54.709
LGA    I    35_A      I    35_A     1.613     0    0.058   1.328     4.276   79.405   71.667
LGA    A    36_A      A    36_A     0.425     0    0.047   0.055     0.894   97.619   98.095
LGA    E    37_A      E    37_A     0.757     0    0.063   0.770     4.815   90.476   71.058
LGA    R    38_A      R    38_A     0.651     0    0.030   1.059     2.886   95.238   75.411
LGA    E    39_A      E    39_A     0.264     0    0.031   0.173     1.421   97.619   93.704
LGA    Q    40_A      Q    40_A     0.772     0    0.029   0.767     2.507   88.333   81.852
LGA    G    41_A      G    41_A     1.339     0    0.098   0.098     1.883   79.286   79.286
LGA    E    42_A      E    42_A     0.786     0    0.184   1.078     3.103   90.476   76.561
LGA    G    43_A      G    43_A     1.427     0    0.082   0.082     1.511   79.286   79.286
LGA    E    44_A      E    44_A     1.374     0    0.113   0.830     3.687   83.690   70.952
LGA    F    45_A      F    45_A     2.122     0    0.068   1.433     9.635   66.786   36.104
LGA    D    46_A      D    46_A     2.554     0    0.069   0.871     3.203   64.881   62.024
LGA    E    47_A      E    47_A     1.648     0    0.072   0.834     4.178   79.405   66.614
LGA    C    48_A      C    48_A     0.830     0    0.030   0.172     1.256   90.595   89.048
LGA    L    49_A      L    49_A     0.829     0    0.059   1.400     4.761   92.857   75.774
LGA    E    50_A      E    50_A     0.757     0    0.034   0.984     4.457   90.476   75.132
LGA    A    51_A      A    51_A     0.598     0    0.047   0.048     0.602   90.476   90.476
LGA    L    52_A      L    52_A     0.664     0    0.062   1.419     3.257   90.476   79.048
LGA    D    53_A      D    53_A     0.869     0    0.028   0.938     4.571   90.476   72.143
LGA    D    54_A      D    54_A     0.593     0    0.039   1.153     4.429   92.857   78.571
LGA    A    55_A      A    55_A     0.267     0    0.031   0.048     0.454  100.000  100.000
LGA    K    56_A      K    56_A     0.737     0    0.062   0.636     2.964   92.857   83.122
LGA    R    57_A      R    57_A     1.431     0    0.120   1.080     4.770   79.286   69.394
LGA    A    58_A      A    58_A     1.181     0    0.150   0.151     1.773   79.286   79.714
LGA    L    59_A      L    59_A     0.854     0    0.546   1.480     2.993   83.810   77.500
LGA    P    60_A      P    60_A     3.386     0    0.053   0.254     7.528   48.571   35.578

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     1.879          1.773                  2.931           80.427   70.097

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     59    1.70    84.167    91.886     3.270

LGA_LOCAL      RMSD:   1.704  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.890  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.879  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.527641 * X  +   0.258362 * Y  +  -0.809224 * Z  +  25.256994
  Y_new =   0.623519 * X  +  -0.764757 * Y  +   0.162390 * Z  +  -6.826724
  Z_new =  -0.576904 * X  +  -0.590250 * Y  +  -0.564611 * Z  +   5.363192 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.868494  0.614934 -2.333997   [DEG:   49.7611   35.2331 -133.7282 ]
ZXZ: -1.768840  2.170758 -2.367629   [DEG: -101.3471  124.3753 -135.6551 ]
 
# END of job
