 
####################################################### 
#                                                     # 
#                        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 420 atoms, 380 common with TARGET 
           Number of atoms possible to evaluate: 342 
 
 
 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 . . . . . . . . . .    90.39           31.4   140    93.3   150     ARMSMC  
     WELL ORDERED  . . . . .    90.39           31.4   140    93.3   150     ARMSMC  
     NO INTER CONTACTS . . .    90.39           31.4   140    93.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    90.51           29.7   128    92.8   138     ARMSMC  
     ALTERNATIVE PARENT  . .    93.26           10.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    67.71           50.0    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   101.73           25.0    52    83.9    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    99.94           26.0    96    90.6   106     ARMSMC  
     BURIED  . . . . . . . .    64.86           43.2    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    82.97           35.2    88   100.0    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) =  -0.05875     r(1,2) =  -0.47546     r(1,3) =   0.87777 
 r(2,1) =   0.29056     r(2,2) =  -0.84936     r(2,3) =  -0.44063 
 r(3,1) =   0.95505     r(3,2) =   0.22916     r(3,3) =   0.18805 
THE OFFSET VECTOR: 
 v(1) =  14.30974     v(2) =  35.91547     v(3) = -45.23510 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.65           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   15.50         71    93.4    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2183                            CRMSCA  
     WELL ORDERED  . . . . .   15.50         71    93.4    76     CRMSCA  
     NO INTER CONTACTS . . .   15.50         71    93.4    76     CRMSCA  
     SHIFTED CHAIN . . . . .   14.63         65    92.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .   18.79          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   16.95         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .   17.69          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   16.24         27    84.4    32     CRMSCA  
     SURFACE . . . . . . . .   16.45         49    90.7    54     CRMSCA  
     BURIED  . . . . . . . .   13.13         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .   15.02         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   15.62        342    92.2   371     CRMSMC  
     WELL ORDERED  . . . . .   15.62        342    92.2   371     CRMSMC  
     NO INTER CONTACTS . . .   15.62        342    92.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   14.67        312    91.5   341     CRMSMC  
     ALTERNATIVE PARENT  . .   18.83         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   17.09        132    99.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .   17.65         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   16.34        127    82.5   154     CRMSMC  
     SURFACE . . . . . . . .   16.61        236    89.4   264     CRMSMC  
     BURIED  . . . . . . . .   13.17        106    99.1   107     CRMSMC  
     CORE  . . . . . . . . .   15.19        215    99.1   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   16.32         58    20.4   284     CRMSSC  
     WELL ORDERED  . . . . .   16.32         58    20.4   284     CRMSSC  
     NO INTER CONTACTS . . .   16.32         58    20.4   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   16.32         58    24.2   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   17.35         24    24.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   16.96         19    17.0   112     CRMSSC  
     SURFACE . . . . . . . .   17.42         40    18.0   222     CRMSSC  
     BURIED  . . . . . . . .   13.55         18    29.0    62     CRMSSC  
     CORE  . . . . . . . . .   16.00         39    22.7   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   15.62        342    58.2   588     CRMSALL 
     WELL ORDERED  . . . . .   15.62        342    58.2   588     CRMSALL 
     NO INTER CONTACTS . . .   15.62        342    58.2   588     CRMSALL 
     SHIFTED CHAIN . . . . .   14.67        312    57.6   542     CRMSALL 
     ALTERNATIVE PARENT  . .   18.83         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .   17.09        132    63.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   16.34        127    52.9   240     CRMSALL 
     SURFACE . . . . . . . .   16.61        236    53.9   438     CRMSALL 
     BURIED  . . . . . . . .   13.17        106    70.7   150     CRMSALL 
     CORE  . . . . . . . . .   15.19        215    61.8   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     9.58      2    28.6     7       1-AEIEVGR-7    
 CA  LOOP  2     5.48      3   100.0     3      26-GGG-28   
 CA  LOOP  3    12.43     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    24.33      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     9.70      9    26.5    34       1-AEIEVGR-7    
 MC  LOOP  2     5.79     12   100.0    12      26-GGG-28   
 MC  LOOP  3    12.42     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    23.95     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     9.70      9    17.0    53       1-AEIEVGR-7    
 ALL LOOP  2     5.79     12   100.0    12      26-GGG-28   
 ALL LOOP  3    12.42     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    23.95     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.49      3   100.0     3      26-GGG-28   
 CA  LOOP  3     5.40     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.33      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.83     12   100.0    12      26-GGG-28   
 MC  LOOP  3     5.60     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.07     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.83     12   100.0    12      26-GGG-28   
 ALL LOOP  3     5.60     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.07     19    54.3    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 . . . . . . . . . .   13.267      1.000       0.500     71    93.4    76     ERRCA  
     WELL ORDERED  . . . . .   13.267      1.000       0.500     71    93.4    76     ERRCA  
     NO INTER CONTACTS . . .   13.267      1.000       0.500     71    93.4    76     ERRCA  
     SHIFTED CHAIN . . . . .   12.447      1.000       0.500     65    92.9    70     ERRCA  
     ALTERNATIVE PARENT  . .   17.576      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .   15.312      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   14.203      1.000       0.500     27    84.4    32     ERRCA  
     SURFACE . . . . . . . .   13.941      1.000       0.500     49    90.7    54     ERRCA  
     BURIED  . . . . . . . .   11.765      1.000       0.500     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .   12.693      1.000       0.500     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.427      1.000       0.500    342    92.2   371     ERRMC  
     WELL ORDERED  . . . . .   13.427      1.000       0.500    342    92.2   371     ERRMC  
     NO INTER CONTACTS . . .   13.427      1.000       0.500    342    92.2   371     ERRMC  
     SHIFTED CHAIN . . . . .   12.539      1.000       0.500    312    91.5   341     ERRMC  
     ALTERNATIVE PARENT  . .   17.473      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .   15.431      1.000       0.500    132    99.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   14.378      1.000       0.500    127    82.5   154     ERRMC  
     SURFACE . . . . . . . .   14.231      1.000       0.500    236    89.4   264     ERRMC  
     BURIED  . . . . . . . .   11.637      1.000       0.500    106    99.1   107     ERRMC  
     CORE  . . . . . . . . .   12.865      1.000       0.500    215    99.1   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.158      1.000       0.500     58    20.4   284     ERRSC  
     WELL ORDERED  . . . . .   14.158      1.000       0.500     58    20.4   284     ERRSC  
     NO INTER CONTACTS . . .   14.158      1.000       0.500     58    20.4   284     ERRSC  
     RELIABLE SIDE CHAINS  .   14.158      1.000       0.500     58    24.2   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   13.165      1.000       0.500     52    19.8   262     ERRSC  
     ALTERNATIVE PARENT  . .   17.543      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .   15.574      1.000       0.500     24    24.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   15.121      1.000       0.500     19    17.0   112     ERRSC  
     SURFACE . . . . . . . .   15.152      1.000       0.500     40    18.0   222     ERRSC  
     BURIED  . . . . . . . .   11.949      1.000       0.500     18    29.0    62     ERRSC  
     CORE  . . . . . . . . .   13.689      1.000       0.500     39    22.7   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.427      1.000       0.500    342    58.2   588     ERRALL 
     WELL ORDERED  . . . . .   13.427      1.000       0.500    342    58.2   588     ERRALL 
     NO INTER CONTACTS . . .   13.427      1.000       0.500    342    58.2   588     ERRALL 
     SHIFTED CHAIN . . . . .   12.539      1.000       0.500    312    57.6   542     ERRALL 
     ALTERNATIVE PARENT  . .   17.473      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .   15.431      1.000       0.500    132    63.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   14.378      1.000       0.500    127    52.9   240     ERRALL 
     SURFACE . . . . . . . .   14.231      1.000       0.500    236    53.9   438     ERRALL 
     BURIED  . . . . . . . .   11.637      1.000       0.500    106    70.7   150     ERRALL 
     CORE  . . . . . . . . .   12.865      1.000       0.500    215    61.8   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)         1         5         6        12        29      71      76   DISTCA 
CA  (P)      1.32      6.58      7.89     15.79     38.16              76   DISTCA 
CA  (RMS)    0.58      1.43      1.65      3.45      6.53                   DISTCA 
 
ALL (N)         4        12        26        49       140     342     588   DISTALL 
ALL (P)      0.68      2.04      4.42      8.33     23.81             588   DISTALL 
ALL (RMS)    0.65      1.37      2.11      3.25      6.65                   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            44            27          RMSLSI 
CA  (P)       57.89         57.89         35.53          RMSLSI 
CA  (RMS)      1.67         15.02         16.24          RMSLSI 
 
 
 
END of the results output 
