 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0047.inter 
# 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0047.1mup.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0047.1obp_A.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0047.1beb_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0047.1epa_B.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 1287 atoms, MODEL 1304 atoms, 1275 common with TARGET 
           Number of atoms possible to evaluate: 1267 
 
 
 CA-RMS TARGET<->PARENT(1mup)	 1.202822 
 
 CA-RMS TARGET<->PARENT(1obp-A)	 2.128074 
 
 CA-RMS TARGET<->PARENT(1beb-A)	 2.195152 
 
 CA-RMS TARGET<->PARENT(1epa-B)	 1.899896 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    34.32           88.5   312    99.4   314     ARMSMC  
     WELL ORDERED  . . . . .    20.48           94.2   190   100.0   190     ARMSMC  
     NO INTER CONTACTS . . .    33.70           88.7   292    99.3   294     ARMSMC  
     SHIFTED CHAIN . . . . .    55.73           68.9    61    96.8    63     ARMSMC  
     ALTERNATIVE PARENT  . .    53.35           50.0    14   100.0    14     ARMSMC  
     SECONDARY STRUCTURE . .    15.81           95.1   162   100.0   162     ARMSMC  
     LARGE SHIFTS/INSERTIONS    81.12           52.4    21    95.5    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    43.14           83.4   163    99.4   164     ARMSMC  
     BURIED  . . . . . . . .    20.76           94.0   149    99.3   150     ARMSMC  
     CORE  . . . . . . . . .    28.08           91.1   291    99.7   292     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.56           56.9   137    97.2   141     ARMSSC1 
     WELL ORDERED  . . . . .    65.13           64.4    59   100.0    59     ARMSSC1 
     NO INTER CONTACTS . . .    69.68           59.8   127    96.9   131     ARMSSC1 
     RELIABLE SIDE CHAINS  .    70.76           57.0   128    97.0   132     ARMSSC1 
     CHANGED ANGLES  . . . .   105.29            6.5    62    95.4    65     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.69           38.5    26    92.9    28     ARMSSC1 
     ALTERNATIVE PARENT  . .    47.76           80.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    75.09           57.3    75   100.0    75     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    74.88           44.4     9   100.0     9     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    88.29           37.0    73    94.8    77     ARMSSC1 
     BURIED  . . . . . . . .    45.52           79.7    64   100.0    64     ARMSSC1 
     CORE  . . . . . . . . .    71.32           57.8   128    97.0   132     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    65.83           55.1   107    96.4   111     ARMSSC2 
     WELL ORDERED  . . . . .    50.32           63.6    44   100.0    44     ARMSSC2 
     NO INTER CONTACTS . . .    66.75           56.6    99    96.1   103     ARMSSC2 
     RELIABLE SIDE CHAINS  .    64.48           54.9    82    97.6    84     ARMSSC2 
     CHANGED ANGLES  . . . .    85.76           21.7    60    93.8    64     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.34           44.4    18    90.0    20     ARMSSC2 
     ALTERNATIVE PARENT  . .   119.26            0.0     5   100.0     5     ARMSSC2 
     SECONDARY STRUCTURE . .    61.50           61.0    59   100.0    59     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    82.64           28.6     7   100.0     7     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    66.71           45.0    60    93.8    64     ARMSSC2 
     BURIED  . . . . . . . .    64.69           68.1    47   100.0    47     ARMSSC2 
     CORE  . . . . . . . . .    64.49           57.0   100    96.2   104     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.98           41.5    41    95.3    43     ARMSSC3 
     WELL ORDERED  . . . . .   100.56            0.0     7   100.0     7     ARMSSC3 
     NO INTER CONTACTS . . .    69.14           44.4    36    94.7    38     ARMSSC3 
     RELIABLE SIDE CHAINS  .    72.79           43.6    39    95.1    41     ARMSSC3 
     CHANGED ANGLES  . . . .    81.95           27.3    33    94.3    35     ARMSSC3 
     SHIFTED CHAIN . . . . .    73.12           50.0    12    92.3    13     ARMSSC3 
     ALTERNATIVE PARENT  . .    53.22           33.3     3   100.0     3     ARMSSC3 
     SECONDARY STRUCTURE . .    79.88           25.0    20   100.0    20     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    69.87           40.0     5   100.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    69.04           41.9    31    93.9    33     ARMSSC3 
     BURIED  . . . . . . . .    87.53           40.0    10   100.0    10     ARMSSC3 
     CORE  . . . . . . . . .    74.53           41.7    36    94.7    38     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.87           31.8    22   100.0    22     ARMSSC4 
     WELL ORDERED  . . . . .    47.34           25.0     4   100.0     4     ARMSSC4 
     NO INTER CONTACTS . . .    78.64           27.8    18   100.0    18     ARMSSC4 
     RELIABLE SIDE CHAINS  .    72.87           31.8    22   100.0    22     ARMSSC4 
     CHANGED ANGLES  . . . .    77.84           21.1    19   100.0    19     ARMSSC4 
     SHIFTED CHAIN . . . . .    73.26           28.6     7   100.0     7     ARMSSC4 
     ALTERNATIVE PARENT  . .    30.34            0.0     1   100.0     1     ARMSSC4 
     SECONDARY STRUCTURE . .    62.05           40.0    10   100.0    10     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    72.22            0.0     3   100.0     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    69.68           29.4    17   100.0    17     ARMSSC4 
     BURIED  . . . . . . . .    82.80           40.0     5   100.0     5     ARMSSC4 
     CORE  . . . . . . . . .    72.97           36.8    19   100.0    19     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.71187     r(1,2) =   0.68342     r(1,3) =   0.16179 
 r(2,1) =  -0.70080     r(2,2) =   0.70633     r(2,3) =   0.09984 
 r(3,1) =  -0.04605     r(3,2) =  -0.18445     r(3,3) =   0.98176 
THE OFFSET VECTOR: 
 v(1) =  41.46310     v(2) =  20.53162     v(3) =  -6.21555 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.69           (Number of atoms:  146) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.30        157    99.4   158     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0083                            CRMSCA  
     WELL ORDERED  . . . . .    0.70         95   100.0    95     CRMSCA  
     NO INTER CONTACTS . . .    1.29        147    99.3   148     CRMSCA  
     SHIFTED CHAIN . . . . .    2.75         31    96.9    32     CRMSCA  
     ALTERNATIVE PARENT  . .    4.39          7   100.0     7     CRMSCA  
     SECONDARY STRUCTURE . .    0.57         81   100.0    81     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.21         11   100.0    11     CRMSCA  
     SURFACE . . . . . . . .    1.63         82    98.8    83     CRMSCA  
     BURIED  . . . . . . . .    0.80         75   100.0    75     CRMSCA  
     CORE  . . . . . . . . .    0.69        146    99.3   147     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.35        773    99.2   779     CRMSMC  
     WELL ORDERED  . . . . .    0.69        453   100.0   453     CRMSMC  
     NO INTER CONTACTS . . .    1.35        723    99.2   729     CRMSMC  
     SHIFTED CHAIN . . . . .    2.82        150    96.2   156     CRMSMC  
     ALTERNATIVE PARENT  . .    4.30         33   100.0    33     CRMSMC  
     SECONDARY STRUCTURE . .    0.65        402   100.0   402     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.27         53   100.0    53     CRMSMC  
     SURFACE . . . . . . . .    1.68        405    98.5   411     CRMSMC  
     BURIED  . . . . . . . .    0.87        368   100.0   368     CRMSMC  
     CORE  . . . . . . . . .    0.79        720    99.2   726     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.54        639    97.6   655     CRMSSC  
     WELL ORDERED  . . . . .    1.90        321   100.0   321     CRMSSC  
     NO INTER CONTACTS . . .    2.52        590    97.4   606     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.53        561    97.9   573     CRMSSC  
     CHANGED ANGLES  . . . .    3.48        294    95.8   307     CRMSSC  
     SECONDARY STRUCTURE . .    2.23        357   100.0   357     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.83         42   100.0    42     CRMSSC  
     SURFACE . . . . . . . .    3.17        344    95.6   360     CRMSSC  
     BURIED  . . . . . . . .    1.48        295   100.0   295     CRMSSC  
     CORE  . . . . . . . . .    2.12        597    97.4   613     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.03       1267    98.4  1287     CRMSALL 
     WELL ORDERED  . . . . .    1.39        701   100.0   701     CRMSALL 
     NO INTER CONTACTS . . .    2.01       1178    98.3  1198     CRMSALL 
     SHIFTED CHAIN . . . . .    3.45        233    94.7   246     CRMSALL 
     ALTERNATIVE PARENT  . .    5.23         51   100.0    51     CRMSALL 
     SECONDARY STRUCTURE . .    1.67        681   100.0   681     CRMSALL 
     LARGE SHIFTS/INSERTIONS    5.03         86   100.0    86     CRMSALL 
     SURFACE . . . . . . . .    2.54        672    97.1   692     CRMSALL 
     BURIED  . . . . . . . .    1.21        595   100.0   595     CRMSALL 
     CORE  . . . . . . . . .    1.60       1181    98.3  1201     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.25      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     3.71      5   100.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.13     19   100.0    19      60-ENGE-63   
 MC  LOOP  2     3.94     25   100.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.66     30   100.0    30      60-ENGE-63   
 ALL LOOP  2     5.20     41   100.0    41     153-KTDRC-157  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.14      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     1.74      5   100.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.38     19   100.0    19      60-ENGE-63   
 MC  LOOP  2     2.24     25   100.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.62     30   100.0    30      60-ENGE-63   
 ALL LOOP  2     3.77     41   100.0    41     153-KTDRC-157  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.710      0.386       0.410    157    99.4   158     ERRCA  
     WELL ORDERED  . . . . .    0.568      0.393       0.444     95   100.0    95     ERRCA  
     NO INTER CONTACTS . . .    0.709      0.388       0.416    147    99.3   148     ERRCA  
     SHIFTED CHAIN . . . . .    1.364      0.318       0.163     31    96.9    32     ERRCA  
     ALTERNATIVE PARENT  . .    3.119      0.572       0.286      7   100.0     7     ERRCA  
     SECONDARY STRUCTURE . .    0.568      0.413       0.473     81   100.0    81     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.024      0.579       0.290     11   100.0    11     ERRCA  
     SURFACE . . . . . . . .    0.804      0.362       0.366     82    98.8    83     ERRCA  
     BURIED  . . . . . . . .    0.608      0.412       0.458     75   100.0    75     ERRCA  
     CORE  . . . . . . . . .    0.536      0.371       0.419    146    99.3   147     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.712      0.375       0.389    773    99.2   779     ERRMC  
     WELL ORDERED  . . . . .    0.543      0.380       0.428    453   100.0   453     ERRMC  
     NO INTER CONTACTS . . .    0.708      0.376       0.393    723    99.2   729     ERRMC  
     SHIFTED CHAIN . . . . .    1.447      0.341       0.186    150    96.2   156     ERRMC  
     ALTERNATIVE PARENT  . .    3.008      0.554       0.277     33   100.0    33     ERRMC  
     SECONDARY STRUCTURE . .    0.550      0.391       0.442    402   100.0   402     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.051      0.577       0.289     53   100.0    53     ERRMC  
     SURFACE . . . . . . . .    0.807      0.353       0.343    405    98.5   411     ERRMC  
     BURIED  . . . . . . . .    0.607      0.399       0.440    368   100.0   368     ERRMC  
     CORE  . . . . . . . . .    0.540      0.360       0.397    720    99.2   726     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.204      0.358       0.278    639    97.6   655     ERRSC  
     WELL ORDERED  . . . . .    0.872      0.330       0.283    321   100.0   321     ERRSC  
     NO INTER CONTACTS . . .    1.189      0.358       0.283    590    97.4   606     ERRSC  
     RELIABLE SIDE CHAINS  .    1.204      0.360       0.284    561    97.9   573     ERRSC  
     CHANGED ANGLES  . . . .    1.942      0.417       0.236    294    95.8   307     ERRSC  
     SHIFTED CHAIN . . . . .    2.371      0.426       0.222    109    92.4   118     ERRSC  
     ALTERNATIVE PARENT  . .    4.635      0.641       0.321     23   100.0    23     ERRSC  
     SECONDARY STRUCTURE . .    1.068      0.361       0.296    357   100.0   357     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.199      0.611       0.307     42   100.0    42     ERRSC  
     SURFACE . . . . . . . .    1.634      0.383       0.252    344    95.6   360     ERRSC  
     BURIED  . . . . . . . .    0.703      0.330       0.309    295   100.0   295     ERRSC  
     CORE  . . . . . . . . .    0.994      0.340       0.276    597    97.4   613     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.963      0.371       0.340   1267    98.4  1287     ERRALL 
     WELL ORDERED  . . . . .    0.702      0.361       0.367    701   100.0   701     ERRALL 
     NO INTER CONTACTS . . .    0.952      0.371       0.345   1178    98.3  1198     ERRALL 
     SHIFTED CHAIN . . . . .    1.858      0.381       0.204    233    94.7   246     ERRALL 
     ALTERNATIVE PARENT  . .    3.702      0.590       0.295     51   100.0    51     ERRALL 
     SECONDARY STRUCTURE . .    0.828      0.380       0.373    681   100.0   681     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.561      0.592       0.297     86   100.0    86     ERRALL 
     SURFACE . . . . . . . .    1.232      0.374       0.305    672    97.1   692     ERRALL 
     BURIED  . . . . . . . .    0.658      0.368       0.380    595   100.0   595     ERRALL 
     CORE  . . . . . . . . .    0.773      0.355       0.343   1181    98.3  1201     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)       133       143       148       155       157     157     158   DISTCA 
CA  (P)     84.18     90.51     93.67     98.10     99.37             158   DISTCA 
CA  (RMS)    0.51      0.63      0.75      1.10      1.30                   DISTCA 
 
ALL (N)       844      1015      1119      1216      1266    1267    1287   DISTALL 
ALL (P)     65.58     78.87     86.95     94.48     98.37            1287   DISTALL 
ALL (RMS)    0.54      0.78      1.06      1.49      2.00                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)         147           146            11          RMSLSI 
CA  (P)       93.04         92.41          6.96          RMSLSI 
CA  (RMS)      0.77          0.69          4.21          RMSLSI 
 
 
 
END of the results output 
