 
####################################################### 
#                                                     # 
#                        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 1339 atoms, 1286 common with TARGET 
           Number of atoms possible to evaluate: 1254 
 
 
 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 . . . . . . . . . .    32.87           85.6   306    97.5   314     ARMSMC  
     WELL ORDERED  . . . . .    19.42           93.7   189    99.5   190     ARMSMC  
     NO INTER CONTACTS . . .    32.06           87.1   286    97.3   294     ARMSMC  
     SHIFTED CHAIN . . . . .    53.76           61.0    59    93.7    63     ARMSMC  
     ALTERNATIVE PARENT  . .    53.08           50.0    14   100.0    14     ARMSMC  
     SECONDARY STRUCTURE . .    16.91           92.0   162   100.0   162     ARMSMC  
     LARGE SHIFTS/INSERTIONS    76.08           52.6    19    86.4    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    42.56           80.0   160    97.6   164     ARMSMC  
     BURIED  . . . . . . . .    16.74           91.8   146    97.3   150     ARMSMC  
     CORE  . . . . . . . . .    27.73           87.8   287    98.3   292     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.06           51.1   137    97.2   141     ARMSSC1 
     WELL ORDERED  . . . . .    65.83           59.3    59   100.0    59     ARMSSC1 
     NO INTER CONTACTS . . .    71.10           51.2   127    96.9   131     ARMSSC1 
     RELIABLE SIDE CHAINS  .    69.43           50.8   128    97.0   132     ARMSSC1 
     CHANGED ANGLES  . . . .    92.20           26.6    64    98.5    65     ARMSSC1 
     SHIFTED CHAIN . . . . .    84.86           26.9    26    92.9    28     ARMSSC1 
     ALTERNATIVE PARENT  . .    66.83           20.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    71.76           58.7    75   100.0    75     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    85.43           25.0     8    88.9     9     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    84.35           33.8    74    96.1    77     ARMSSC1 
     BURIED  . . . . . . . .    48.13           71.4    63    98.4    64     ARMSSC1 
     CORE  . . . . . . . . .    68.99           52.7   129    97.7   132     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.12           50.9   108    97.3   111     ARMSSC2 
     WELL ORDERED  . . . . .    53.34           65.9    44   100.0    44     ARMSSC2 
     NO INTER CONTACTS . . .    72.00           51.0   100    97.1   103     ARMSSC2 
     RELIABLE SIDE CHAINS  .    67.50           52.4    82    97.6    84     ARMSSC2 
     CHANGED ANGLES  . . . .    87.91           37.7    61    95.3    64     ARMSSC2 
     SHIFTED CHAIN . . . . .    77.85           36.8    19    95.0    20     ARMSSC2 
     ALTERNATIVE PARENT  . .    77.74           60.0     5   100.0     5     ARMSSC2 
     SECONDARY STRUCTURE . .    64.21           61.0    59   100.0    59     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    45.61           57.1     7   100.0     7     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    74.94           42.6    61    95.3    64     ARMSSC2 
     BURIED  . . . . . . . .    63.32           61.7    47   100.0    47     ARMSSC2 
     CORE  . . . . . . . . .    71.51           50.5   101    97.1   104     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.42           36.6    41    95.3    43     ARMSSC3 
     WELL ORDERED  . . . . .    86.31           42.9     7   100.0     7     ARMSSC3 
     NO INTER CONTACTS . . .    68.29           36.1    36    94.7    38     ARMSSC3 
     RELIABLE SIDE CHAINS  .    72.22           38.5    39    95.1    41     ARMSSC3 
     CHANGED ANGLES  . . . .    76.72           35.3    34    97.1    35     ARMSSC3 
     SHIFTED CHAIN . . . . .    65.94           46.2    13   100.0    13     ARMSSC3 
     ALTERNATIVE PARENT  . .    98.69           33.3     3   100.0     3     ARMSSC3 
     SECONDARY STRUCTURE . .    74.49           25.0    20   100.0    20     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    77.08           60.0     5   100.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    69.51           32.3    31    93.9    33     ARMSSC3 
     BURIED  . . . . . . . .    80.80           50.0    10   100.0    10     ARMSSC3 
     CORE  . . . . . . . . .    71.75           33.3    36    94.7    38     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.14           27.3    22   100.0    22     ARMSSC4 
     WELL ORDERED  . . . . .    63.77           25.0     4   100.0     4     ARMSSC4 
     NO INTER CONTACTS . . .    89.07           27.8    18   100.0    18     ARMSSC4 
     RELIABLE SIDE CHAINS  .    85.14           27.3    22   100.0    22     ARMSSC4 
     CHANGED ANGLES  . . . .    86.61           26.3    19   100.0    19     ARMSSC4 
     SHIFTED CHAIN . . . . .    60.56           57.1     7   100.0     7     ARMSSC4 
     ALTERNATIVE PARENT  . .    14.20          100.0     1   100.0     1     ARMSSC4 
     SECONDARY STRUCTURE . .    93.45           20.0    10   100.0    10     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    50.32           33.3     3   100.0     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    94.12           23.5    17   100.0    17     ARMSSC4 
     BURIED  . . . . . . . .    42.16           40.0     5   100.0     5     ARMSSC4 
     CORE  . . . . . . . . .    89.41           26.3    19   100.0    19     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.02642     r(1,2) =  -0.38752     r(1,3) =   0.92148 
 r(2,1) =   0.83710     r(2,2) =   0.49528     r(2,3) =   0.23228 
 r(3,1) =  -0.54641     r(3,2) =   0.77752     r(3,3) =   0.31130 
THE OFFSET VECTOR: 
 v(1) =  72.15449     v(2) =  20.64354     v(3) =  22.00549 
 
 Number of iteration 22                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.83           (Number of atoms:  142) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.38        154    97.5   158     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0090                            CRMSCA  
     WELL ORDERED  . . . . .    0.95         95   100.0    95     CRMSCA  
     NO INTER CONTACTS . . .    1.34        144    97.3   148     CRMSCA  
     SHIFTED CHAIN . . . . .    2.74         30    93.8    32     CRMSCA  
     ALTERNATIVE PARENT  . .    4.06          7   100.0     7     CRMSCA  
     SECONDARY STRUCTURE . .    0.75         81   100.0    81     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.18         10    90.9    11     CRMSCA  
     SURFACE . . . . . . . .    1.70         80    96.4    83     CRMSCA  
     BURIED  . . . . . . . .    0.91         74    98.7    75     CRMSCA  
     CORE  . . . . . . . . .    0.91        144    98.0   147     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.43        758    97.3   779     CRMSMC  
     WELL ORDERED  . . . . .    0.91        452    99.8   453     CRMSMC  
     NO INTER CONTACTS . . .    1.39        708    97.1   729     CRMSMC  
     SHIFTED CHAIN . . . . .    2.81        145    92.9   156     CRMSMC  
     ALTERNATIVE PARENT  . .    4.09         33   100.0    33     CRMSMC  
     SECONDARY STRUCTURE . .    0.83        402   100.0   402     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.27         47    88.7    53     CRMSMC  
     SURFACE . . . . . . . .    1.76        396    96.4   411     CRMSMC  
     BURIED  . . . . . . . .    0.94        362    98.4   368     CRMSMC  
     CORE  . . . . . . . . .    0.99        711    97.9   726     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.54        639    97.6   655     CRMSSC  
     WELL ORDERED  . . . . .    1.99        321   100.0   321     CRMSSC  
     NO INTER CONTACTS . . .    2.49        590    97.4   606     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.51        559    97.6   573     CRMSSC  
     CHANGED ANGLES  . . . .    3.32        298    97.1   307     CRMSSC  
     SECONDARY STRUCTURE . .    2.29        357   100.0   357     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.14         40    95.2    42     CRMSSC  
     SURFACE . . . . . . . .    3.10        346    96.1   360     CRMSSC  
     BURIED  . . . . . . . .    1.64        293    99.3   295     CRMSSC  
     CORE  . . . . . . . . .    2.26        599    97.7   613     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.06       1254    97.4  1287     CRMSALL 
     WELL ORDERED  . . . . .    1.50        700    99.9   701     CRMSALL 
     NO INTER CONTACTS . . .    2.01       1165    97.2  1198     CRMSALL 
     SHIFTED CHAIN . . . . .    3.42        231    93.9   246     CRMSALL 
     ALTERNATIVE PARENT  . .    4.57         51   100.0    51     CRMSALL 
     SECONDARY STRUCTURE . .    1.75        681   100.0   681     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.68         79    91.9    86     CRMSALL 
     SURFACE . . . . . . . .    2.53        666    96.2   692     CRMSALL 
     BURIED  . . . . . . . .    1.32        588    98.8   595     CRMSALL 
     CORE  . . . . . . . . .    1.74       1175    97.8  1201     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.79      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     4.02      4    80.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.78     19   100.0    19      60-ENGE-63   
 MC  LOOP  2     4.16     19    76.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.24     30   100.0    30      60-ENGE-63   
 ALL LOOP  2     4.69     34    82.9    41     153-KTDRC-157  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.20      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     1.64      4    80.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.63     19   100.0    19      60-ENGE-63   
 MC  LOOP  2     2.15     19    76.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.96     30   100.0    30      60-ENGE-63   
 ALL LOOP  2     3.69     34    82.9    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 . . . . . . . . . .    0.647      0.328       0.330    154    97.5   158     ERRCA  
     WELL ORDERED  . . . . .    0.555      0.355       0.395     95   100.0    95     ERRCA  
     NO INTER CONTACTS . . .    0.630      0.328       0.334    144    97.3   148     ERRCA  
     SHIFTED CHAIN . . . . .    1.394      0.332       0.181     30    93.8    32     ERRCA  
     ALTERNATIVE PARENT  . .    2.836      0.555       0.277      7   100.0     7     ERRCA  
     SECONDARY STRUCTURE . .    0.520      0.365       0.400     81   100.0    81     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.024      0.582       0.291     10    90.9    11     ERRCA  
     SURFACE . . . . . . . .    0.726      0.286       0.250     80    96.4    83     ERRCA  
     BURIED  . . . . . . . .    0.561      0.374       0.416     74    98.7    75     ERRCA  
     CORE  . . . . . . . . .    0.482      0.311       0.333    144    98.0   147     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.647      0.314       0.302    758    97.3   779     ERRMC  
     WELL ORDERED  . . . . .    0.506      0.325       0.347    452    99.8   453     ERRMC  
     NO INTER CONTACTS . . .    0.629      0.313       0.305    708    97.1   729     ERRMC  
     SHIFTED CHAIN . . . . .    1.452      0.345       0.194    145    92.9   156     ERRMC  
     ALTERNATIVE PARENT  . .    2.844      0.549       0.274     33   100.0    33     ERRMC  
     SECONDARY STRUCTURE . .    0.514      0.346       0.367    402   100.0   402     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.078      0.583       0.292     47    88.7    53     ERRMC  
     SURFACE . . . . . . . .    0.752      0.286       0.242    396    96.4   411     ERRMC  
     BURIED  . . . . . . . .    0.533      0.345       0.368    362    98.4   368     ERRMC  
     CORE  . . . . . . . . .    0.487      0.296       0.303    711    97.9   726     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.229      0.353       0.252    639    97.6   655     ERRSC  
     WELL ORDERED  . . . . .    0.938      0.348       0.289    321   100.0   321     ERRSC  
     NO INTER CONTACTS . . .    1.198      0.351       0.254    590    97.4   606     ERRSC  
     RELIABLE SIDE CHAINS  .    1.211      0.350       0.252    559    97.6   573     ERRSC  
     CHANGED ANGLES  . . . .    1.867      0.415       0.237    298    97.1   307     ERRSC  
     SHIFTED CHAIN . . . . .    2.491      0.471       0.238    112    94.9   118     ERRSC  
     ALTERNATIVE PARENT  . .    3.571      0.587       0.293     23   100.0    23     ERRSC  
     SECONDARY STRUCTURE . .    1.100      0.354       0.267    357   100.0   357     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.625      0.587       0.293     40    95.2    42     ERRSC  
     SURFACE . . . . . . . .    1.627      0.376       0.224    346    96.1   360     ERRSC  
     BURIED  . . . . . . . .    0.759      0.327       0.285    293    99.3   295     ERRSC  
     CORE  . . . . . . . . .    1.069      0.338       0.249    599    97.7   613     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.938      0.335       0.280   1254    97.4  1287     ERRALL 
     WELL ORDERED  . . . . .    0.705      0.337       0.323    700    99.9   701     ERRALL 
     NO INTER CONTACTS . . .    0.914      0.334       0.283   1165    97.2  1198     ERRALL 
     SHIFTED CHAIN . . . . .    1.928      0.404       0.217    231    93.9   246     ERRALL 
     ALTERNATIVE PARENT  . .    3.161      0.565       0.283     51   100.0    51     ERRALL 
     SECONDARY STRUCTURE . .    0.822      0.354       0.322    681   100.0   681     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.318      0.584       0.292     79    91.9    86     ERRALL 
     SURFACE . . . . . . . .    1.198      0.332       0.234    666    96.2   692     ERRALL 
     BURIED  . . . . . . . .    0.644      0.339       0.331    588    98.8   595     ERRALL 
     CORE  . . . . . . . . .    0.779      0.318       0.279   1175    97.8  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)       108       141       145       151       154     154     158   DISTCA 
CA  (P)     68.35     89.24     91.77     95.57     97.47             158   DISTCA 
CA  (RMS)    0.56      0.81      0.91      1.15      1.38                   DISTCA 
 
ALL (N)       686       981      1097      1203      1253    1254    1287   DISTALL 
ALL (P)     53.30     76.22     85.24     93.47     97.36            1287   DISTALL 
ALL (RMS)    0.59      0.92      1.20      1.61      2.03                   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           144            10          RMSLSI 
CA  (P)       93.04         91.14          6.33          RMSLSI 
CA  (RMS)      0.77          0.91          4.18          RMSLSI 
 
 
 
END of the results output 
