 
####################################################### 
#                                                     # 
#                        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/T0001.inter 
CONANA-PAIR            ../CONANA/T0001.pair 
# 
NUMBER-OF-PARENTS      5 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0001.4dfr_B.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0001.3dfr.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp2.T0001.8dfr.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp2.T0001.1drf.rot 
ALIGNMENT-DALI(5)      ../PARENTS/casp2.T0001.1dyr.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 1211 atoms, MODEL 1264 atoms, 1209 common with TARGET 
           Number of atoms possible to evaluate: 1192 
 
 
 CA-RMS TARGET<->PARENT(4dfr_B)	 1.747068 
 
 CA-RMS TARGET<->PARENT(3dfr)	 1.763903 
 
 CA-RMS TARGET<->PARENT(8dfr)	 1.949174 
 
 CA-RMS TARGET<->PARENT(1drf)	 2.143564 
 
 CA-RMS TARGET<->PARENT(1dyr)	 1.942374 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    47.56           76.6   308    98.7   312     ARMSMC  
     WELL ORDERED  . . . . .    27.27           87.9   199   100.0   199     ARMSMC  
     NO INTER CONTACTS . . .    46.66           75.6   246    99.2   248     ARMSMC  
     SHIFTED CHAIN . . . . .    56.60           71.4   192   100.0   192     ARMSMC  
     ALTERNATIVE PARENT  . .    70.29           65.9    44   100.0    44     ARMSMC  
     SECONDARY STRUCTURE . .    19.44           90.1   171    98.3   174     ARMSMC  
     LARGE SHIFTS/INSERTIONS    79.55           48.1    52   100.0    52     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    52.82           72.7   172    97.7   176     ARMSMC  
     BURIED  . . . . . . . .    39.93           81.6   136   100.0   136     ARMSMC  
     CORE  . . . . . . . . .    37.90           82.4   256    98.5   260     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.10           55.3   123    98.4   125     ARMSSC1 
     WELL ORDERED  . . . . .    63.90           55.4    65   100.0    65     ARMSSC1 
     NO INTER CONTACTS . . .    68.84           57.7    97    99.0    98     ARMSSC1 
     RELIABLE SIDE CHAINS  .    71.36           52.7   110    98.2   112     ARMSSC1 
     CHANGED ANGLES  . . . .    82.70           38.8    67    97.1    69     ARMSSC1 
     SHIFTED CHAIN . . . . .    75.37           47.2    72   100.0    72     ARMSSC1 
     ALTERNATIVE PARENT  . .    94.63           29.4    17   100.0    17     ARMSSC1 
     SECONDARY STRUCTURE . .    64.62           58.0    69    98.6    70     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    84.73           47.6    21   100.0    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    72.53           51.4    70    97.2    72     ARMSSC1 
     BURIED  . . . . . . . .    66.75           60.4    53   100.0    53     ARMSSC1 
     CORE  . . . . . . . . .    66.69           56.9   102    98.1   104     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.62           45.6    90    97.8    92     ARMSSC2 
     WELL ORDERED  . . . . .    75.61           52.3    44   100.0    44     ARMSSC2 
     NO INTER CONTACTS . . .    72.16           50.0    66    98.5    67     ARMSSC2 
     RELIABLE SIDE CHAINS  .    67.08           46.1    76    98.7    77     ARMSSC2 
     CHANGED ANGLES  . . . .    85.09           32.1    56    98.2    57     ARMSSC2 
     SHIFTED CHAIN . . . . .    81.97           36.4    55   100.0    55     ARMSSC2 
     ALTERNATIVE PARENT  . .    86.73           15.4    13   100.0    13     ARMSSC2 
     SECONDARY STRUCTURE . .    78.68           50.0    48    98.0    49     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    88.72           13.3    15   100.0    15     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    80.01           34.0    53    96.4    55     ARMSSC2 
     BURIED  . . . . . . . .    60.50           62.2    37   100.0    37     ARMSSC2 
     CORE  . . . . . . . . .    68.96           52.0    75    97.4    77     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    66.63           18.8    32    97.0    33     ARMSSC3 
     WELL ORDERED  . . . . .    78.25            0.0    11   100.0    11     ARMSSC3 
     NO INTER CONTACTS . . .    63.76           19.0    21   100.0    21     ARMSSC3 
     RELIABLE SIDE CHAINS  .    64.15           21.4    28    96.6    29     ARMSSC3 
     CHANGED ANGLES  . . . .    66.27           20.7    29    96.7    30     ARMSSC3 
     SHIFTED CHAIN . . . . .    72.62           20.0    20   100.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .    72.81           20.0     5   100.0     5     ARMSSC3 
     SECONDARY STRUCTURE . .    70.91           15.0    20    95.2    21     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    52.53           20.0     5   100.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    67.04           25.0    24    96.0    25     ARMSSC3 
     BURIED  . . . . . . . .    65.39            0.0     8   100.0     8     ARMSSC3 
     CORE  . . . . . . . . .    68.93           18.5    27    96.4    28     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   100.93           16.7    12    92.3    13     ARMSSC4 
     WELL ORDERED  . . . . .   102.71           25.0     4    80.0     5     ARMSSC4 
     NO INTER CONTACTS . . .   110.82           12.5     8   100.0     8     ARMSSC4 
     RELIABLE SIDE CHAINS  .   100.93           16.7    12    92.3    13     ARMSSC4 
     CHANGED ANGLES  . . . .   100.93           16.7    12    92.3    13     ARMSSC4 
     SHIFTED CHAIN . . . . .    79.97           12.5     8   100.0     8     ARMSSC4 
     ALTERNATIVE PARENT  . .    79.98            0.0     3   100.0     3     ARMSSC4 
     SECONDARY STRUCTURE . .    99.30           12.5     8    88.9     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   111.21            0.0     1   100.0     1     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   107.43           20.0    10    90.9    11     ARMSSC4 
     BURIED  . . . . . . . .    58.41            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    99.94           18.2    11    91.7    12     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.47382     r(1,2) =  -0.19245     r(1,3) =   0.85934 
 r(2,1) =   0.29141     r(2,2) =  -0.95512     r(2,3) =  -0.05322 
 r(3,1) =   0.83101     r(3,2) =   0.22521     r(3,3) =   0.50863 
THE OFFSET VECTOR: 
 v(1) =  19.48657     v(2) =  48.45784     v(3) = -10.89138 
 
 Number of iteration 38                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.26           (Number of atoms:  135) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.02        155    98.7   157     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0130                            CRMSCA  
     WELL ORDERED  . . . . .    1.40        105   100.0   105     CRMSCA  
     NO INTER CONTACTS . . .    1.86        124    99.2   125     CRMSCA  
     SHIFTED CHAIN . . . . .    2.49         96   100.0    96     CRMSCA  
     ALTERNATIVE PARENT  . .    3.22         22   100.0    22     CRMSCA  
     SECONDARY STRUCTURE . .    1.19         86    98.9    87     CRMSCA  
     SHIFTED SS UNITS  . . .    1.51         28   100.0    28     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.90         26   100.0    26     CRMSCA  
     SURFACE . . . . . . . .    2.37         87    97.8    89     CRMSCA  
     BURIED  . . . . . . . .    1.45         68   100.0    68     CRMSCA  
     CORE  . . . . . . . . .    1.35        129    98.5   131     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.08        763    98.7   773     CRMSMC  
     WELL ORDERED  . . . . .    1.44        499   100.0   499     CRMSMC  
     NO INTER CONTACTS . . .    1.89        609    99.2   614     CRMSMC  
     SHIFTED CHAIN . . . . .    2.57        470   100.0   470     CRMSMC  
     ALTERNATIVE PARENT  . .    3.43        107   100.0   107     CRMSMC  
     SECONDARY STRUCTURE . .    1.23        426    98.8   431     CRMSMC  
     SHIFTED SS UNITS  . . .    1.55        138   100.0   138     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.02        127   100.0   127     CRMSMC  
     SURFACE . . . . . . . .    2.47        429    97.7   439     CRMSMC  
     BURIED  . . . . . . . .    1.43        334   100.0   334     CRMSMC  
     CORE  . . . . . . . . .    1.41        636    98.5   646     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.25        572    98.1   583     CRMSSC  
     WELL ORDERED  . . . . .    2.64        322    98.2   328     CRMSSC  
     NO INTER CONTACTS . . .    2.99        426    99.1   430     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.28        504    98.2   513     CRMSSC  
     CHANGED ANGLES  . . . .    3.95        300    97.7   307     CRMSSC  
     SECONDARY STRUCTURE . .    2.17        321    97.9   328     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.51         89   100.0    89     CRMSSC  
     SURFACE . . . . . . . .    3.75        316    96.6   327     CRMSSC  
     BURIED  . . . . . . . .    2.48        256   100.0   256     CRMSSC  
     CORE  . . . . . . . . .    2.63        483    97.8   494     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.67       1192    98.4  1211     CRMSALL 
     WELL ORDERED  . . . . .    2.03        731    99.2   737     CRMSALL 
     NO INTER CONTACTS . . .    2.43        922    99.1   930     CRMSALL 
     SHIFTED CHAIN . . . . .    3.23        720   100.0   720     CRMSALL 
     ALTERNATIVE PARENT  . .    4.70        165   100.0   165     CRMSALL 
     SECONDARY STRUCTURE . .    1.74        665    98.4   676     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.68        193   100.0   193     CRMSALL 
     SURFACE . . . . . . . .    3.10        664    97.2   683     CRMSALL 
     BURIED  . . . . . . . .    2.00        528   100.0   528     CRMSALL 
     CORE  . . . . . . . . .    2.07        999    98.1  1018     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.87      9   100.0     9      50-ESMRDDLPG-58   
 CA  LOOP  2     5.08      8   100.0     8      68-ERSFSVDT-75   
 CA  LOOP  3     1.93      3   100.0     3      91-SLD-93   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.88     43   100.0    43      50-ESMRDDLPG-58   
 MC  LOOP  2     5.25     40   100.0    40      68-ERSFSVDT-75   
 MC  LOOP  3     2.15     15   100.0    15      91-SLD-93   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.39     62   100.0    62      50-ESMRDDLPG-58   
 ALL LOOP  2     6.17     65   100.0    65      68-ERSFSVDT-75   
 ALL LOOP  3     2.59     22   100.0    22      91-SLD-93   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.88      9   100.0     9      50-ESMRDDLPG-58   
 CA  LOOP  2     2.35      8   100.0     8      68-ERSFSVDT-75   
 CA  LOOP  3     0.36      3   100.0     3      91-SLD-93   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.04     43   100.0    43      50-ESMRDDLPG-58   
 MC  LOOP  2     2.66     40   100.0    40      68-ERSFSVDT-75   
 MC  LOOP  3     1.01     15   100.0    15      91-SLD-93   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.72     62   100.0    62      50-ESMRDDLPG-58   
 ALL LOOP  2     4.24     65   100.0    65      68-ERSFSVDT-75   
 ALL LOOP  3     1.50     22   100.0    22      91-SLD-93   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.190      0.363       0.325    155    98.7   157     ERRCA  
     WELL ORDERED  . . . . .    1.026      0.363       0.372    105   100.0   105     ERRCA  
     NO INTER CONTACTS . . .    1.129      0.367       0.332    124    99.2   125     ERRCA  
     SHIFTED CHAIN . . . . .    1.279      0.327       0.229     96   100.0    96     ERRCA  
     ALTERNATIVE PARENT  . .    1.929      0.419       0.262     22   100.0    22     ERRCA  
     SECONDARY STRUCTURE . .    0.821      0.311       0.339     86    98.9    87     ERRCA  
     LARGE SHIFTS/INSERTIONS    2.432      0.465       0.264     26   100.0    26     ERRCA  
     SURFACE . . . . . . . .    1.291      0.343       0.274     87    97.8    89     ERRCA  
     BURIED  . . . . . . . .    1.061      0.389       0.390     68   100.0    68     ERRCA  
     CORE  . . . . . . . . .    0.940      0.343       0.337    129    98.5   131     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.212      0.367       0.322    763    98.7   773     ERRMC  
     WELL ORDERED  . . . . .    1.030      0.362       0.365    499   100.0   499     ERRMC  
     NO INTER CONTACTS . . .    1.134      0.369       0.329    609    99.2   614     ERRMC  
     SHIFTED CHAIN . . . . .    1.340      0.341       0.240    470   100.0   470     ERRMC  
     ALTERNATIVE PARENT  . .    2.053      0.437       0.268    107   100.0   107     ERRMC  
     SECONDARY STRUCTURE . .    0.810      0.307       0.326    426    98.8   431     ERRMC  
     LARGE SHIFTS/INSERTIONS    2.510      0.477       0.264    127   100.0   127     ERRMC  
     SURFACE . . . . . . . .    1.365      0.357       0.282    429    97.7   439     ERRMC  
     BURIED  . . . . . . . .    1.017      0.380       0.373    334   100.0   334     ERRMC  
     CORE  . . . . . . . . .    0.953      0.345       0.333    636    98.5   646     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.656      0.343       0.285    572    98.1   583     ERRSC  
     WELL ORDERED  . . . . .    1.463      0.353       0.326    322    98.2   328     ERRSC  
     NO INTER CONTACTS . . .    1.567      0.347       0.294    426    99.1   430     ERRSC  
     RELIABLE SIDE CHAINS  .    1.695      0.348       0.293    504    98.2   513     ERRSC  
     CHANGED ANGLES  . . . .    1.992      0.339       0.261    300    97.7   307     ERRSC  
     SHIFTED CHAIN . . . . .    1.965      0.342       0.242    336   100.0   336     ERRSC  
     ALTERNATIVE PARENT  . .    3.622      0.465       0.257     77   100.0    77     ERRSC  
     SECONDARY STRUCTURE . .    1.011      0.279       0.271    321    97.9   328     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.372      0.466       0.247     89   100.0    89     ERRSC  
     SURFACE . . . . . . . .    1.931      0.339       0.255    316    96.6   327     ERRSC  
     BURIED  . . . . . . . .    1.316      0.348       0.322    256   100.0   256     ERRSC  
     CORE  . . . . . . . . .    1.339      0.320       0.292    483    97.8   494     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.409      0.356       0.307   1192    98.4  1211     ERRALL 
     WELL ORDERED  . . . . .    1.208      0.359       0.352    731    99.2   737     ERRALL 
     NO INTER CONTACTS . . .    1.319      0.360       0.316    922    99.1   930     ERRALL 
     SHIFTED CHAIN . . . . .    1.597      0.338       0.240    720   100.0   720     ERRALL 
     ALTERNATIVE PARENT  . .    2.683      0.442       0.260    165   100.0   165     ERRALL 
     SECONDARY STRUCTURE . .    0.914      0.296       0.305    665    98.4   676     ERRALL 
     LARGE SHIFTS/INSERTIONS    2.822      0.466       0.254    193   100.0   193     ERRALL 
     SURFACE . . . . . . . .    1.602      0.346       0.270    664    97.2   683     ERRALL 
     BURIED  . . . . . . . .    1.167      0.369       0.354    528   100.0   528     ERRALL 
     CORE  . . . . . . . . .    1.136      0.335       0.318    999    98.1  1018     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)        64       122       138       147       155     155     157   DISTCA 
CA  (P)     40.76     77.71     87.90     93.63     98.73             157   DISTCA 
CA  (RMS)    0.67      1.09      1.31      1.58      2.02                   DISTCA 
 
ALL (N)       407       811       985      1096      1184    1192    1211   DISTALL 
ALL (P)     33.61     66.97     81.34     90.50     97.77            1211   DISTALL 
ALL (RMS)    0.69      1.13      1.44      1.84      2.52                   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)         131           129            26          RMSLSI 
CA  (P)       83.44         82.17         16.56          RMSLSI 
CA  (RMS)      1.26          1.35          3.90          RMSLSI 
 
 
 
END of the results output 
