
#######################################################
#                                                     #
#                        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   45 (  334),  selected   45 , name one
# Molecule2: number of CA atoms  207 ( 1517),  selected   45 , 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:    27     154_B - 180_B       4.92    22.88
  LCS_AVERAGE:     12.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16     154_B - 169_B       1.91    34.65
  LCS_AVERAGE:      5.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13     154_B - 166_B       0.66    36.45
  LCS_AVERAGE:      4.05

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     L   154_B     L   154_B     13   16   27      9   12   13   13   15   15   15   16   16   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     D   155_B     D   155_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     Q   156_B     Q   156_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     L   157_B     L   157_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     L   158_B     L   158_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     A   159_B     A   159_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     V   160_B     V   160_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     L   161_B     L   161_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     Q   162_B     Q   162_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     E   163_B     E   163_B     13   16   27      9   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     K   164_B     K   164_B     13   16   27      4   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     H   165_B     H   165_B     13   16   27      7   12   13   13   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     K   166_B     K   166_B     13   16   27      4    9   13   13   13   15   15   16   16   16   17   21   23   23   24   26   28   29   30   30 
LCS_GDT     G   167_B     G   167_B      4   16   27      3    4    4    8   15   15   15   16   18   22   22   22   23   25   26   27   28   29   30   30 
LCS_GDT     K   168_B     K   168_B      4   16   27      3    4    4    9   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     P   169_B     P   169_B      3   16   27      3    3    3    9   15   15   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     A   170_B     A   170_B      3    5   27      3    3    3    6    9   13   15   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     T   171_B     T   171_B      7    7   27      5    7    7    7    7    8   10   16   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     T   172_B     T   172_B      7    7   27      5    7    7    7    7    9   12   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     V   173_B     V   173_B      7    7   27      5    7    7    7    7    9   12   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     T   174_B     T   174_B      7    7   27      5    7    7    7   10   10   12   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     Y   175_B     Y   175_B      7    7   27      5    7    7    7    7    9   12   17   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     E   176_B     E   176_B      7    7   27      3    7    7    7    7    7    8    8   10   13   15   18   20   23   24   27   27   28   28   29 
LCS_GDT     I   177_B     I   177_B      7    7   27      4    7    7    7    7    8    9   14   20   22   22   22   24   25   26   27   28   29   30   30 
LCS_GDT     S   178_B     S   178_B      3    4   27      3    3    3    4    5    6    8   11   12   14   18   21   24   25   26   27   28   29   30   30 
LCS_GDT     A   179_B     A   179_B      3    4   27      3    3    3    4    5    5    6    8   11   12   15   20   20   23   26   27   28   29   30   30 
LCS_GDT     E   180_B     E   180_B      3    8   27      3    3    3    4    8    8    8   11   15   17   19   21   24   25   26   27   28   29   30   30 
LCS_GDT     T   181_B     T   181_B      7    9   22      6    7    8    9   10   11   11   13   15   17   19   21   24   25   26   27   28   29   30   30 
LCS_GDT     L   182_B     L   182_B      7    9   22      6    7    8    9   10   11   11   13   14   16   17   20   21   22   23   25   28   29   30   30 
LCS_GDT     R   183_B     R   183_B      7    9   22      6    7    8    9   10   11   11   13   14   16   17   20   21   22   23   24   28   29   30   30 
LCS_GDT     A   184_B     A   184_B      7    9   22      6    7    8    9   10   11   11   13   14   16   17   20   21   22   25   25   28   29   30   30 
LCS_GDT     A   185_B     A   185_B      7    9   22      6    7    8    9   10   11   11   13   14   16   17   20   21   22   23   24   28   29   29   30 
LCS_GDT     V   186_B     V   186_B      7    9   22      6    7    7    9   10   11   11   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     A   187_B     A   187_B      7    9   22      4    7    8    9   10   11   11   13   14   16   17   20   21   22   23   24   25   27   29   30 
LCS_GDT     A   188_B     A   188_B      3    9   22      3    3    4    4    8    9    9   12   14   16   17   20   21   22   23   24   24   26   27   29 
LCS_GDT     L   189_B     L   189_B      3    9   22      3    3    4    4    8    9   10   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     A   190_B     A   190_B      9    9   22      9    9    9    9    9    9    9   12   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     R   191_B     R   191_B      9    9   22      9    9    9    9    9    9   10   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     A   192_B     A   192_B      9    9   22      9    9    9    9    9    9    9   12   14   16   17   20   20   22   23   24   24   25   27   29 
LCS_GDT     A   193_B     A   193_B      9    9   22      9    9    9    9    9    9   11   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     E   194_B     E   194_B      9    9   22      9    9    9    9   10   11   11   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     A   195_B     A   195_B      9    9   22      9    9    9    9    9   11   11   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     A   196_B     A   196_B      9    9   22      9    9    9    9    9   11   11   13   14   16   17   20   21   22   23   24   25   26   27   29 
LCS_GDT     L   197_B     L   197_B      9    9   22      9    9    9    9   10   11   11   12   14   16   17   18   21   22   23   24   25   26   27   29 
LCS_GDT     R   198_B     R   198_B      9    9   22      9    9    9    9   10   10   11   12   13   16   17   18   21   22   23   24   25   26   27   29 
LCS_AVERAGE  LCS_A:   7.12  (   4.05    5.24   12.08 )

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      9     12     13     13     15     15     15     17     20     22     22     22     24     25     26     27     28     29     30     30 
GDT PERCENT_AT   4.35   5.80   6.28   6.28   7.25   7.25   7.25   8.21   9.66  10.63  10.63  10.63  11.59  12.08  12.56  13.04  13.53  14.01  14.49  14.49
GDT RMS_LOCAL    0.24   0.49   0.66   0.66   1.68   1.68   1.67   2.98   3.26   3.51   3.51   3.51   4.40   4.50   4.71   4.90   5.33   5.69   6.04   6.04
GDT RMS_ALL_AT  36.64  36.40  36.45  36.45  33.93  33.93  35.48  24.14  24.63  25.09  25.09  25.09  22.21  22.29  22.00  22.23  20.69  20.15  19.59  19.59

# Checking swapping
#   possible swapping detected:  E   180_B      E   180_B
#   possible swapping detected:  E   194_B      E   194_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L   154_B      L   154_B     6.446     0    0.128   1.298     9.638   21.667   14.643
LGA    D   155_B      D   155_B     2.576     0    0.040   0.088     4.556   63.690   57.381
LGA    Q   156_B      Q   156_B     2.667     0    0.046   0.924     5.239   57.262   45.556
LGA    L   157_B      L   157_B     4.638     0    0.015   0.141     8.421   38.810   24.643
LGA    L   158_B      L   158_B     3.764     0    0.049   0.968     8.631   52.143   32.500
LGA    A   159_B      A   159_B     1.334     0    0.021   0.019     1.924   79.286   78.000
LGA    V   160_B      V   160_B     2.351     0    0.020   0.217     5.163   72.976   56.122
LGA    L   161_B      L   161_B     2.437     0    0.023   0.225     6.495   70.833   49.524
LGA    Q   162_B      Q   162_B     3.291     0    0.036   0.613     8.427   52.024   32.751
LGA    E   163_B      E   163_B     3.686     3    0.127   0.352     4.988   43.810   28.413
LGA    K   164_B      K   164_B     2.356     4    0.105   0.110     2.953   62.857   35.132
LGA    H   165_B      H   165_B     3.208     0    0.417   1.154     4.652   44.405   47.810
LGA    K   166_B      K   166_B     7.565     2    0.613   0.520    12.459    9.762    4.497
LGA    G   167_B      G   167_B     5.233     0    0.240   0.240     5.643   32.024   32.024
LGA    K   168_B      K   168_B     2.193     0    0.493   1.093     3.522   57.381   58.360
LGA    P   169_B      P   169_B     3.190     0    0.266   0.477     5.722   57.381   45.646
LGA    A   170_B      A   170_B     0.288     0    0.580   0.527     2.629   77.857   76.857
LGA    T   171_B      T   171_B     4.722     0    0.616   0.485     7.108   31.548   23.265
LGA    T   172_B      T   172_B     3.599     0    0.121   0.252     6.016   48.452   38.367
LGA    V   173_B      V   173_B     3.496     0    0.013   0.259     6.870   50.119   36.735
LGA    T   174_B      T   174_B     4.039     0    0.036   0.155     7.731   36.429   26.190
LGA    Y   175_B      Y   175_B     3.557     0    0.082   1.119    11.225   36.548   24.008
LGA    E   176_B      E   176_B     8.149     0    0.616   0.864    15.923   10.476    4.656
LGA    I   177_B      I   177_B     4.871     0    0.206   1.149     7.066   21.071   41.786
LGA    S   178_B      S   178_B     7.262     0    0.177   0.589     7.789   12.976   13.730
LGA    A   179_B      A   179_B    11.511     0    0.587   0.592    14.114    0.000    0.000
LGA    E   180_B      E   180_B    11.205     0    0.574   1.065    13.672    0.000    2.804
LGA    T   181_B      T   181_B    11.986     0    0.619   0.555    15.381    0.000    0.408
LGA    L   182_B      L   182_B    18.720     0    0.034   0.383    21.894    0.000    0.000
LGA    R   183_B      R   183_B    22.287     0    0.107   1.334    25.565    0.000    0.000
LGA    A   184_B      A   184_B    18.474     0    0.013   0.017    21.585    0.000    0.000
LGA    A   185_B      A   185_B    21.472     0    0.188   0.190    26.174    0.000    0.000
LGA    V   186_B      V   186_B    28.057     0    0.163   0.162    31.807    0.000    0.000
LGA    A   187_B      A   187_B    28.512     0    0.600   0.586    31.131    0.000    0.000
LGA    A   188_B      A   188_B    31.912     0    0.572   0.580    33.098    0.000    0.000
LGA    L   189_B      L   189_B    35.139     0    0.621   0.881    38.556    0.000    0.000
LGA    A   190_B      A   190_B    36.457     0    0.600   0.594    39.872    0.000    0.000
LGA    R   191_B      R   191_B    40.558     0    0.100   0.994    44.158    0.000    0.000
LGA    A   192_B      A   192_B    42.412     0    0.055   0.061    45.164    0.000    0.000
LGA    A   193_B      A   193_B    42.395     0    0.016   0.022    46.093    0.000    0.000
LGA    E   194_B      E   194_B    46.591     0    0.027   1.072    50.625    0.000    0.000
LGA    A   195_B      A   195_B    50.105     0    0.053   0.060    53.559    0.000    0.000
LGA    A   196_B      A   196_B    50.729     0    0.107   0.115    53.565    0.000    0.000
LGA    L   197_B      L   197_B    52.330     0    0.198   0.367    56.144    0.000    0.000
LGA    R   198_B      R   198_B    57.393     0    0.551   0.705    60.088    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     325    325  100.00               207
SUMMARY(RMSD_GDC):    12.167         12.035                 12.548            5.516    4.501

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45  207    4.0     17    2.98     8.333     7.711     0.553

LGA_LOCAL      RMSD:   2.977  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  24.141  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:  12.167  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.258277 * X  +   0.805193 * Y  +  -0.533814 * Z  + -77.431000
  Y_new =   0.285269 * X  +  -0.591488 * Y  +  -0.754164 * Z  +  21.183563
  Z_new =  -0.922992 * X  +   0.042502 * Y  +  -0.382465 * Z  +  -7.202403 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.835017  1.175785  3.030919   [DEG:   47.8429   67.3675  173.6589 ]
ZXZ: -0.615957  1.963259 -1.524780   [DEG:  -35.2917  112.4864  -87.3635 ]
 
# END of job
