
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   39 , 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:    39       4_B - 42_B        1.20     1.20
  LCS_AVERAGE:     95.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       4_B - 42_B        1.20     1.20
  LCS_AVERAGE:     95.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       4_B - 39_B        0.99     1.23
  LCS_AVERAGE:     84.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     4_B     Q     4_B     36   39   39      3   20   27   35   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R     5_B     R     5_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_B     L     6_B     36   39   39      5   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F     7_B     F     7_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V     8_B     V     8_B     36   39   39      5   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     9_B     L     9_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    10_B     D    10_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     N    11_B     N    11_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    12_B     E    12_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    13_B     R    13_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    14_B     Y    14_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    15_B     D    15_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    16_B     S    16_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    17_B     F    17_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    18_B     I    18_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     T    19_B     T    19_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q    20_B     Q    20_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    21_B     L    21_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    22_B     E    22_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    23_B     A    23_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     P    24_B     P    24_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    25_B     V    25_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q    26_B     Q    26_B     36   39   39      9   26   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     N    27_B     N    27_B     36   39   39      9   18   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    28_B     A    28_B     36   39   39     10   18   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    29_B     E    29_B     36   39   39     10   16   27   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    30_B     G    30_B     36   39   39     10   19   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    31_B     R    31_B     36   39   39     10   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    32_B     E    32_B     36   39   39     16   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    33_B     R    33_B     36   39   39     10   26   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    34_B     L    34_B     36   39   39     10   26   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    35_B     M    35_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    36_B     A    36_B     36   39   39     16   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    37_B     V    37_B     36   39   39     16   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    38_B     K    38_B     36   39   39     17   27   32   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     P    39_B     P    39_B     36   39   39      4   15   28   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    40_B     E    40_B     27   39   39      4    7   19   29   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W    41_B     W    41_B     24   39   39      4   15   22   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    42_B     K    42_B      4   39   39      3    3    4   15   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  91.58  (  84.49   95.12   95.12 )

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     17     27     32     36     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  41.46  65.85  78.05  87.80  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12
GDT RMS_LOCAL    0.25   0.55   0.77   1.00   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20
GDT RMS_ALL_AT   2.51   1.25   1.23   1.22   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    29_B      E    29_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    Q     4_B      Q     4_B     2.223     0    0.625   0.773    10.243   61.905   34.709
LGA    R     5_B      R     5_B     0.850     0    0.102   0.339     2.791   88.214   77.186
LGA    L     6_B      L     6_B     0.831     0    0.059   0.107     1.610   95.238   87.262
LGA    F     7_B      F     7_B     0.403     0    0.066   0.128     1.175   95.238   88.918
LGA    V     8_B      V     8_B     0.802     0    0.012   1.175     2.698   90.476   80.748
LGA    L     9_B      L     9_B     0.616     0    0.054   0.131     1.183   90.476   87.083
LGA    D    10_B      D    10_B     0.592     0    0.035   0.443     1.723   92.857   86.131
LGA    N    11_B      N    11_B     0.324     0    0.061   0.883     2.394   95.238   87.440
LGA    E    12_B      E    12_B     1.104     0    0.029   0.970     4.475   83.690   68.148
LGA    R    13_B      R    13_B     1.157     0    0.039   1.036     3.200   83.690   73.377
LGA    Y    14_B      Y    14_B     0.321     0    0.059   0.138     1.577  100.000   90.714
LGA    D    15_B      D    15_B     0.339     0    0.020   0.457     1.525  100.000   90.774
LGA    S    16_B      S    16_B     0.688     0    0.019   0.788     2.771   90.476   84.921
LGA    F    17_B      F    17_B     0.388     0    0.026   0.266     1.570  100.000   89.913
LGA    I    18_B      I    18_B     0.168     0    0.032   0.109     0.663  100.000   98.810
LGA    T    19_B      T    19_B     0.428     0    0.012   0.225     1.370  100.000   94.626
LGA    Q    20_B      Q    20_B     0.475     0    0.030   0.805     2.154  100.000   89.947
LGA    L    21_B      L    21_B     0.618     0    0.028   0.256     2.248   92.857   83.036
LGA    E    22_B      E    22_B     0.627     0    0.042   0.750     1.715   95.238   87.619
LGA    A    23_B      A    23_B     0.507     0    0.093   0.109     0.696   95.238   94.286
LGA    P    24_B      P    24_B     0.326     0    0.055   0.059     0.570   97.619   98.639
LGA    V    25_B      V    25_B     0.341     0    0.115   1.191     3.142   92.976   82.721
LGA    Q    26_B      Q    26_B     1.132     0    0.025   1.151     5.696   83.690   65.979
LGA    N    27_B      N    27_B     1.906     0    0.059   0.083     2.482   72.857   68.810
LGA    A    28_B      A    28_B     1.661     0    0.119   0.132     1.787   75.000   74.571
LGA    E    29_B      E    29_B     2.178     0    0.070   0.519     4.076   68.810   59.312
LGA    G    30_B      G    30_B     1.723     0    0.105   0.105     1.935   77.143   77.143
LGA    R    31_B      R    31_B     0.761     0    0.041   1.262     4.605   90.476   75.368
LGA    E    32_B      E    32_B     0.705     0    0.097   0.762     2.916   90.476   80.212
LGA    R    33_B      R    33_B     1.331     0    0.036   1.049     3.868   83.690   72.900
LGA    L    34_B      L    34_B     1.203     0    0.020   1.362     4.847   83.690   64.940
LGA    M    35_B      M    35_B     0.657     0    0.027   0.545     1.576   90.476   87.143
LGA    A    36_B      A    36_B     0.507     0    0.014   0.028     0.870   97.619   96.190
LGA    V    37_B      V    37_B     0.471     0    0.077   0.096     1.216   92.976   89.320
LGA    K    38_B      K    38_B     0.647     4    0.100   0.116     1.734   86.190   47.354
LGA    P    39_B      P    39_B     1.744     0    0.091   0.334     1.935   75.000   77.823
LGA    E    40_B      E    40_B     2.761     0    0.317   0.308     6.089   64.881   44.868
LGA    W    41_B      W    41_B     2.264     0    0.137   0.294     4.600   55.595   47.619
LGA    K    42_B      K    42_B     2.581     0    0.149   0.992     3.041   65.000   64.286

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     325    325  100.00                41
SUMMARY(RMSD_GDC):     1.204          1.194                  2.089           82.805   74.411

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   41    4.0     39    1.20    85.976    91.025     2.991

LGA_LOCAL      RMSD:   1.204  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.204  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   1.204  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.905616 * X  +  -0.404699 * Y  +  -0.126801 * Z  +  19.180578
  Y_new =   0.407227 * X  +  -0.746318 * Y  +  -0.526474 * Z  + -11.860600
  Z_new =   0.118430 * X  +  -0.528420 * Y  +   0.840682 * Z  +  34.160881 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.719014 -0.118708 -0.561156   [DEG:  155.7881   -6.8015  -32.1519 ]
ZXZ: -0.236348  0.572255  2.921116   [DEG:  -13.5417   32.7878  167.3676 ]
 
# END of job
