 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0004.1csp.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0004.1mjc.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 588 atoms, MODEL 433 atoms, 376 common with TARGET 
           Number of atoms possible to evaluate: 331 
 
 
 CA-RMS TARGET<->PARENT(1csp)	 2.141282 
 
 CA-RMS TARGET<->PARENT(1mjc)	 2.434782 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.46           37.7   138    92.0   150     ARMSMC  
     WELL ORDERED  . . . . .    85.46           37.7   138    92.0   150     ARMSMC  
     NO INTER CONTACTS . . .    85.46           37.7   138    92.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    86.43           37.8   127    92.0   138     ARMSMC  
     ALTERNATIVE PARENT  . .   102.60           20.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    73.27           47.2    53    98.1    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   102.56           34.0    53    85.5    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    90.52           35.8    95    89.6   106     ARMSMC  
     BURIED  . . . . . . . .    73.03           41.9    43    97.7    44     ARMSMC  
     CORE  . . . . . . . . .    72.79           40.0    85    96.6    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    46     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.85385     r(1,2) =  -0.34397     r(1,3) =   0.39066 
 r(2,1) =  -0.50961     r(2,2) =   0.70522     r(2,3) =  -0.49291 
 r(3,1) =  -0.10596     r(3,2) =  -0.61996     r(3,3) =  -0.77745 
THE OFFSET VECTOR: 
 v(1) =  21.74290     v(2) =   1.07030     v(3) =  44.72027 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.69           (Number of atoms:    8) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   24.60         70    92.1    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3515                            CRMSCA  
     WELL ORDERED  . . . . .   24.60         70    92.1    76     CRMSCA  
     NO INTER CONTACTS . . .   24.60         70    92.1    76     CRMSCA  
     SHIFTED CHAIN . . . . .   24.73         64    91.4    70     CRMSCA  
     ALTERNATIVE PARENT  . .   27.74          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   26.06         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .   19.82          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   26.89         27    84.4    32     CRMSCA  
     SURFACE . . . . . . . .   25.35         48    88.9    54     CRMSCA  
     BURIED  . . . . . . . .   22.89         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .   23.05         43    97.7    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   24.33        331    89.2   371     CRMSMC  
     WELL ORDERED  . . . . .   24.33        331    89.2   371     CRMSMC  
     NO INTER CONTACTS . . .   24.33        331    89.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   24.45        304    89.1   341     CRMSMC  
     ALTERNATIVE PARENT  . .   27.68         24    96.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   25.69        128    96.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .   20.01         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   26.54        125    81.2   154     CRMSMC  
     SURFACE . . . . . . . .   25.21        227    86.0   264     CRMSMC  
     BURIED  . . . . . . . .   22.29        104    97.2   107     CRMSMC  
     CORE  . . . . . . . . .   22.89        206    94.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   23.11         51    18.0   284     CRMSSC  
     WELL ORDERED  . . . . .   23.11         51    18.0   284     CRMSSC  
     NO INTER CONTACTS . . .   23.11         51    18.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   23.11         51    21.2   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   24.94         20    20.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   24.34         17    15.2   112     CRMSSC  
     SURFACE . . . . . . . .   24.54         35    15.8   222     CRMSSC  
     BURIED  . . . . . . . .   19.62         16    25.8    62     CRMSSC  
     CORE  . . . . . . . . .   22.46         34    19.8   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   24.33        331    56.3   588     CRMSALL 
     WELL ORDERED  . . . . .   24.33        331    56.3   588     CRMSALL 
     NO INTER CONTACTS . . .   24.33        331    56.3   588     CRMSALL 
     SHIFTED CHAIN . . . . .   24.45        304    56.1   542     CRMSALL 
     ALTERNATIVE PARENT  . .   27.68         24    53.3    45     CRMSALL 
     SECONDARY STRUCTURE . .   25.69        128    61.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   26.54        125    52.1   240     CRMSALL 
     SURFACE . . . . . . . .   25.21        227    51.8   438     CRMSALL 
     BURIED  . . . . . . . .   22.29        104    69.3   150     CRMSALL 
     CORE  . . . . . . . . .   22.89        206    59.2   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    55.53      4    57.1     7       1-AEIEVGR-7    
 CA  LOOP  2    19.60      3   100.0     3      26-GGG-28   
 CA  LOOP  3    14.44     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     4.98      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    55.33     18    52.9    34       1-AEIEVGR-7    
 MC  LOOP  2    20.20     12   100.0    12      26-GGG-28   
 MC  LOOP  3    14.59     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     4.79     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    55.33     18    34.0    53       1-AEIEVGR-7    
 ALL LOOP  2    20.20     12   100.0    12      26-GGG-28   
 ALL LOOP  3    14.59     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     4.79     18    51.4    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.70      4    57.1     7       1-AEIEVGR-7    
 CA  LOOP  2     0.06      3   100.0     3      26-GGG-28   
 CA  LOOP  3     7.69     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.14      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.40     18    52.9    34       1-AEIEVGR-7    
 MC  LOOP  2     1.76     12   100.0    12      26-GGG-28   
 MC  LOOP  3     7.97     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.94     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.40     18    34.0    53       1-AEIEVGR-7    
 ALL LOOP  2     1.76     12   100.0    12      26-GGG-28   
 ALL LOOP  3     7.97     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.94     18    51.4    35      65-RQGR-68   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   20.428      1.000       0.500     70    92.1    76     ERRCA  
     WELL ORDERED  . . . . .   20.428      1.000       0.500     70    92.1    76     ERRCA  
     NO INTER CONTACTS . . .   20.428      1.000       0.500     70    92.1    76     ERRCA  
     SHIFTED CHAIN . . . . .   20.314      1.000       0.500     64    91.4    70     ERRCA  
     ALTERNATIVE PARENT  . .   19.698      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .   23.399      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   20.249      1.000       0.500     27    84.4    32     ERRCA  
     SURFACE . . . . . . . .   20.610      1.000       0.500     48    88.9    54     ERRCA  
     BURIED  . . . . . . . .   20.029      1.000       0.500     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .   20.540      1.000       0.500     43    97.7    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   20.219      1.000       0.500    331    89.2   371     ERRMC  
     WELL ORDERED  . . . . .   20.219      1.000       0.500    331    89.2   371     ERRMC  
     NO INTER CONTACTS . . .   20.219      1.000       0.500    331    89.2   371     ERRMC  
     SHIFTED CHAIN . . . . .   20.106      1.000       0.500    304    89.1   341     ERRMC  
     ALTERNATIVE PARENT  . .   19.608      1.000       0.500     24    96.0    25     ERRMC  
     SECONDARY STRUCTURE . .   23.087      1.000       0.500    128    96.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   19.887      1.000       0.500    125    81.2   154     ERRMC  
     SURFACE . . . . . . . .   20.526      1.000       0.500    227    86.0   264     ERRMC  
     BURIED  . . . . . . . .   19.550      1.000       0.500    104    97.2   107     ERRMC  
     CORE  . . . . . . . . .   20.420      1.000       0.500    206    94.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   19.208      1.000       0.500     51    18.0   284     ERRSC  
     WELL ORDERED  . . . . .   19.208      1.000       0.500     51    18.0   284     ERRSC  
     NO INTER CONTACTS . . .   19.208      1.000       0.500     51    18.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .   19.208      1.000       0.500     51    21.2   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   19.000      1.000       0.500     48    18.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   19.693      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .   22.281      1.000       0.500     20    20.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   17.743      1.000       0.500     17    15.2   112     ERRSC  
     SURFACE . . . . . . . .   20.013      1.000       0.500     35    15.8   222     ERRSC  
     BURIED  . . . . . . . .   17.447      1.000       0.500     16    25.8    62     ERRSC  
     CORE  . . . . . . . . .   19.940      1.000       0.500     34    19.8   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   20.219      1.000       0.500    331    56.3   588     ERRALL 
     WELL ORDERED  . . . . .   20.219      1.000       0.500    331    56.3   588     ERRALL 
     NO INTER CONTACTS . . .   20.219      1.000       0.500    331    56.3   588     ERRALL 
     SHIFTED CHAIN . . . . .   20.106      1.000       0.500    304    56.1   542     ERRALL 
     ALTERNATIVE PARENT  . .   19.608      1.000       0.500     24    53.3    45     ERRALL 
     SECONDARY STRUCTURE . .   23.087      1.000       0.500    128    61.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   19.887      1.000       0.500    125    52.1   240     ERRALL 
     SURFACE . . . . . . . .   20.526      1.000       0.500    227    51.8   438     ERRALL 
     BURIED  . . . . . . . .   19.550      1.000       0.500    104    69.3   150     ERRALL 
     CORE  . . . . . . . . .   20.420      1.000       0.500    206    59.2   348     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)         2         6         8        13        17      70      76   DISTCA 
CA  (P)      2.63      7.89     10.53     17.11     22.37              76   DISTCA 
CA  (RMS)    0.70      1.40      1.69      2.95      4.34                   DISTCA 
 
ALL (N)        11        23        36        60        84     331     588   DISTALL 
ALL (P)      1.87      3.91      6.12     10.20     14.29             588   DISTALL 
ALL (RMS)    0.76      1.19      1.78      2.85      4.47                   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)          44            43            27          RMSLSI 
CA  (P)       57.89         56.58         35.53          RMSLSI 
CA  (RMS)      1.67         23.05         26.89          RMSLSI 
 
 
 
END of the results output 
