 
####################################################### 
#                                                     # 
#                        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/T0009.inter 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0009.2cbp.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) 
 
           TARGET 837 atoms, MODEL 837 atoms, 837 common with TARGET 
           Number of atoms possible to evaluate: 742 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    87.71           38.2   186    86.9   214     ARMSMC  
     WELL ORDERED  . . . . .    85.91           40.4   156    86.2   181     ARMSMC  
     NO INTER CONTACTS . . .    85.65           39.2   143    87.2   164     ARMSMC  
     SHIFTED CHAIN . . . . .    89.85           36.0   100    90.9   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    84.65           34.2    73    91.2    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS    84.50           35.0    40    87.0    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    90.73           32.7   113    85.6   132     ARMSMC  
     BURIED  . . . . . . . .    82.83           46.6    73    89.0    82     ARMSMC  
     CORE  . . . . . . . . .    88.57           39.0   146    86.9   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    92.63           34.5    84    89.4    94     ARMSSC1 
     WELL ORDERED  . . . . .    92.77           31.5    54    85.7    63     ARMSSC1 
     NO INTER CONTACTS . . .    91.79           37.3    67    89.3    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    91.97           33.8    74    90.2    82     ARMSSC1 
     CHANGED ANGLES  . . . .    96.42           41.5    41    87.2    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    95.24           39.5    43    91.5    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    97.10           24.2    33    91.7    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   102.82           26.3    19    90.5    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    88.82           36.0    50    86.2    58     ARMSSC1 
     BURIED  . . . . . . . .    97.96           32.4    34    94.4    36     ARMSSC1 
     CORE  . . . . . . . . .    89.44           36.9    65    89.0    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.05           32.1    56    91.8    61     ARMSSC2 
     WELL ORDERED  . . . . .    73.33           36.7    30    90.9    33     ARMSSC2 
     NO INTER CONTACTS . . .    73.55           29.8    47    92.2    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    61.82           33.3    39    92.9    42     ARMSSC2 
     CHANGED ANGLES  . . . .    74.75           37.1    35    87.5    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    64.63           38.5    26    96.3    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    74.16           32.0    25    92.6    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    52.95           50.0    12    92.3    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    68.48           35.3    34    89.5    38     ARMSSC2 
     BURIED  . . . . . . . .    84.19           27.3    22    95.7    23     ARMSSC2 
     CORE  . . . . . . . . .    80.02           27.3    44    91.7    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.62           29.4    17    94.4    18     ARMSSC3 
     WELL ORDERED  . . . . .    40.29            0.0     3   100.0     3     ARMSSC3 
     NO INTER CONTACTS . . .    74.41           31.2    16    94.1    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    77.43           30.8    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    74.83           25.0    16    94.1    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    90.48           33.3     9    90.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    67.76           30.0    10   100.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    57.24           33.3     3    75.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    76.63           26.7    15    93.8    16     ARMSSC3 
     BURIED  . . . . . . . .    27.95           50.0     2   100.0     2     ARMSSC3 
     CORE  . . . . . . . . .    75.51           28.6    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   113.88           33.3     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .   108.25            0.0     1   100.0     1     ARMSSC4 
     NO INTER CONTACTS . . .   101.93           40.0     5   100.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .   113.88           33.3     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .   100.28           50.0     4   100.0     4     ARMSSC4 
     SHIFTED CHAIN . . . . .    58.09           66.7     3   100.0     3     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   118.08           33.3     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   113.88           33.3     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .   113.88           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.54333     r(1,2) =   0.83393     r(1,3) =   0.09673 
 r(2,1) =   0.10509     r(2,2) =   0.04675     r(2,3) =  -0.99336 
 r(3,1) =  -0.83292     r(3,2) =   0.54989     r(3,3) =  -0.06223 
THE OFFSET VECTOR: 
 v(1) =   8.08509     v(2) =  33.35826     v(3) =  43.63717 
 
 Number of iteration 66                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.60           (Number of atoms:   46) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.46         94    87.0   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0368                            CRMSCA  
     WELL ORDERED  . . . . .    2.87         79    86.8    91     CRMSCA  
     NO INTER CONTACTS . . .    3.45         72    86.7    83     CRMSCA  
     SHIFTED CHAIN . . . . .    3.97         50    89.3    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    3.04         37    92.5    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.97         20    83.3    24     CRMSCA  
     SURFACE . . . . . . . .    3.92         57    85.1    67     CRMSCA  
     BURIED  . . . . . . . .    2.59         37    90.2    41     CRMSCA  
     CORE  . . . . . . . . .    2.91         74    88.1    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.72        465    87.2   533     CRMSMC  
     WELL ORDERED  . . . . .    3.13        383    87.2   439     CRMSMC  
     NO INTER CONTACTS . . .    3.72        357    87.1   410     CRMSMC  
     SHIFTED CHAIN . . . . .    4.21        246    89.1   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    3.32        184    92.5   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.18        100    83.3   120     CRMSMC  
     SURFACE . . . . . . . .    4.18        282    84.9   332     CRMSMC  
     BURIED  . . . . . . . .    2.89        183    91.0   201     CRMSMC  
     CORE  . . . . . . . . .    3.21        365    88.4   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    5.75        366    90.4   405     CRMSSC  
     WELL ORDERED  . . . . .    5.25        242    88.3   274     CRMSSC  
     NO INTER CONTACTS . . .    5.73        296    90.5   327     CRMSSC  
     RELIABLE SIDE CHAINS  .    5.70        296    91.6   323     CRMSSC  
     CHANGED ANGLES  . . . .    6.60        163    88.6   184     CRMSSC  
     SECONDARY STRUCTURE . .    6.10        163    92.6   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.91         74    89.2    83     CRMSSC  
     SURFACE . . . . . . . .    6.06        204    87.2   234     CRMSSC  
     BURIED  . . . . . . . .    5.34        162    94.7   171     CRMSSC  
     CORE  . . . . . . . . .    5.42        292    90.7   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    4.75        742    88.6   837     CRMSALL 
     WELL ORDERED  . . . . .    4.11        557    87.7   635     CRMSALL 
     NO INTER CONTACTS . . .    4.78        584    88.6   659     CRMSALL 
     SHIFTED CHAIN . . . . .    5.22        378    90.6   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    4.90        311    92.6   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    5.98        154    86.0   179     CRMSALL 
     SURFACE . . . . . . . .    5.06        432    86.1   502     CRMSALL 
     BURIED  . . . . . . . .    4.29        310    92.5   335     CRMSALL 
     CORE  . . . . . . . . .    4.38        588    89.4   658     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.33      8   100.0     8      16-PSSPNFYS-23   
 CA  LOOP  2     6.37      8   100.0     8      63-VNSDNDVE-70   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.40     40   100.0    40      16-PSSPNFYS-23   
 MC  LOOP  2     6.69     40   100.0    40      63-VNSDNDVE-70   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.50     63   100.0    63      16-PSSPNFYS-23   
 ALL LOOP  2     7.29     61   100.0    61      63-VNSDNDVE-70   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.73      8   100.0     8      16-PSSPNFYS-23   
 CA  LOOP  2     2.73      8   100.0     8      63-VNSDNDVE-70   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.92     40   100.0    40      16-PSSPNFYS-23   
 MC  LOOP  2     3.43     40   100.0    40      63-VNSDNDVE-70   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.43     63   100.0    63      16-PSSPNFYS-23   
 ALL LOOP  2     4.21     61   100.0    61      63-VNSDNDVE-70   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.078      0.576       0.637     94    87.0   108     ERRCA  
     WELL ORDERED  . . . . .    7.468      0.614       0.678     79    86.8    91     ERRCA  
     NO INTER CONTACTS . . .    7.069      0.575       0.637     72    86.7    83     ERRCA  
     SHIFTED CHAIN . . . . .    6.644      0.531       0.591     50    89.3    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    7.287      0.591       0.658     37    92.5    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.770      0.451       0.499     20    83.3    24     ERRCA  
     SURFACE . . . . . . . .    6.684      0.536       0.601     57    85.1    67     ERRCA  
     BURIED  . . . . . . . .    7.686      0.638       0.694     37    90.2    41     ERRCA  
     CORE  . . . . . . . . .    7.432      0.610       0.675     74    88.1    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.841      0.548       0.612    465    87.2   533     ERRMC  
     WELL ORDERED  . . . . .    7.235      0.587       0.654    383    87.2   439     ERRMC  
     NO INTER CONTACTS . . .    6.819      0.546       0.610    357    87.1   410     ERRMC  
     SHIFTED CHAIN . . . . .    6.431      0.506       0.567    246    89.1   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    7.013      0.558       0.633    184    92.5   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.645      0.434       0.483    100    83.3   120     ERRMC  
     SURFACE . . . . . . . .    6.457      0.510       0.573    282    84.9   332     ERRMC  
     BURIED  . . . . . . . .    7.433      0.608       0.672    183    91.0   201     ERRMC  
     CORE  . . . . . . . . .    7.169      0.580       0.647    365    88.4   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.113      0.379       0.426    366    90.4   405     ERRSC  
     WELL ORDERED  . . . . .    5.492      0.416       0.468    242    88.3   274     ERRSC  
     NO INTER CONTACTS . . .    5.145      0.383       0.429    296    90.5   327     ERRSC  
     RELIABLE SIDE CHAINS  .    5.216      0.390       0.437    296    91.6   323     ERRSC  
     CHANGED ANGLES  . . . .    4.332      0.305       0.337    163    88.6   184     ERRSC  
     SHIFTED CHAIN . . . . .    4.659      0.334       0.372    178    92.2   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    4.794      0.355       0.392    163    92.6   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.407      0.308       0.342     74    89.2    83     ERRSC  
     SURFACE . . . . . . . .    4.787      0.344       0.389    204    87.2   234     ERRSC  
     BURIED  . . . . . . . .    5.523      0.424       0.472    162    94.7   171     ERRSC  
     CORE  . . . . . . . . .    5.292      0.397       0.447    292    90.7   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.070      0.474       0.529    742    88.6   837     ERRALL 
     WELL ORDERED  . . . . .    6.560      0.522       0.582    557    87.7   635     ERRALL 
     NO INTER CONTACTS . . .    6.037      0.471       0.525    584    88.6   659     ERRALL 
     SHIFTED CHAIN . . . . .    5.683      0.434       0.485    378    90.6   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    5.944      0.462       0.516    311    92.6   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.118      0.382       0.423    154    86.0   179     ERRALL 
     SURFACE . . . . . . . .    5.763      0.442       0.497    432    86.1   502     ERRALL 
     BURIED  . . . . . . . .    6.498      0.519       0.573    310    92.5   335     ERRALL 
     CORE  . . . . . . . . .    6.319      0.498       0.556    588    89.4   658     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)        11        35        52        85        94      94     108   DISTCA 
CA  (P)     10.19     32.41     48.15     78.70     87.04             108   DISTCA 
CA  (RMS)    0.74      1.33      1.78      2.77      3.46                   DISTCA 
 
ALL (N)        50       172       301       542       719     742     837   DISTALL 
ALL (P)      5.97     20.55     35.96     64.76     85.90             837   DISTALL 
ALL (RMS)    0.69      1.38      1.94      2.99      4.38                   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)          84            74            20          RMSLSI 
CA  (P)       77.78         68.52         18.52          RMSLSI 
CA  (RMS)      1.02          2.91          4.97          RMSLSI 
 
 
 
END of the results output 
