 
####################################################### 
#                                                     # 
#                        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 593 atoms, 536 common with TARGET 
           Number of atoms possible to evaluate: 94 
 
 
 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 . . . . . . . . . .    60.91           57.7    26    17.3   150     ARMSMC  
     WELL ORDERED  . . . . .    60.91           57.7    26    17.3   150     ARMSMC  
     NO INTER CONTACTS . . .    60.91           57.7    26    17.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    63.01           57.1    21    15.2   138     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    43.72           61.9    21    38.9    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   103.06           25.0     4     6.5    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    74.50           41.7    12    11.3   106     ARMSMC  
     BURIED  . . . . . . . .    46.19           71.4    14    31.8    44     ARMSMC  
     CORE  . . . . . . . . .    49.54           63.6    22    25.0    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) =  -0.18028     r(1,2) =  -0.31761     r(1,3) =   0.93093 
 r(2,1) =   0.62034     r(2,2) =  -0.77119     r(2,3) =  -0.14298 
 r(3,1) =   0.76334     r(3,2) =   0.55171     r(3,3) =   0.33606 
THE OFFSET VECTOR: 
 v(1) =  22.10007     v(2) = -26.52162     v(3) = -83.81728 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.79           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   16.05         19    25.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.8449                            CRMSCA  
     WELL ORDERED  . . . . .   16.05         19    25.0    76     CRMSCA  
     NO INTER CONTACTS . . .   16.05         19    25.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .   17.48         16    22.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   12.36         14    51.9    27     CRMSCA  
     SHIFTED SS UNITS  . . .   16.77          1    16.7     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   13.90          3     9.4    32     CRMSCA  
     SURFACE . . . . . . . .   18.02         10    18.5    54     CRMSCA  
     BURIED  . . . . . . . .   13.53          9    40.9    22     CRMSCA  
     CORE  . . . . . . . . .   16.42         16    36.4    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   16.19         94    25.3   371     CRMSMC  
     WELL ORDERED  . . . . .   16.19         94    25.3   371     CRMSMC  
     NO INTER CONTACTS . . .   16.19         94    25.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .   17.63         79    23.2   341     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   12.57         69    51.9   133     CRMSMC  
     SHIFTED SS UNITS  . . .   17.41          5    16.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   13.74         14     9.1   154     CRMSMC  
     SURFACE . . . . . . . .   17.92         50    18.9   264     CRMSMC  
     BURIED  . . . . . . . .   13.97         44    41.1   107     CRMSMC  
     CORE  . . . . . . . . .   16.58         80    36.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   16.76         18     6.3   284     CRMSSC  
     WELL ORDERED  . . . . .   16.76         18     6.3   284     CRMSSC  
     NO INTER CONTACTS . . .   16.76         18     6.3   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   16.76         18     7.5   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   12.70         13    13.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   16.74          2     1.8   112     CRMSSC  
     SURFACE . . . . . . . .   18.36         10     4.5   222     CRMSSC  
     BURIED  . . . . . . . .   14.51          8    12.9    62     CRMSSC  
     CORE  . . . . . . . . .   16.76         16     9.3   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   16.19         94    16.0   588     CRMSALL 
     WELL ORDERED  . . . . .   16.19         94    16.0   588     CRMSALL 
     NO INTER CONTACTS . . .   16.19         94    16.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .   17.63         79    14.6   542     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0    45     CRMSALL 
     SECONDARY STRUCTURE . .   12.57         69    33.3   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   13.74         14     5.8   240     CRMSALL 
     SURFACE . . . . . . . .   17.92         50    11.4   438     CRMSALL 
     BURIED  . . . . . . . .   13.97         44    29.3   150     CRMSALL 
     CORE  . . . . . . . . .   16.58         80    23.0   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.00      0     0.0     3      26-GGG-28   
 CA  LOOP  3    18.23      1    10.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.00      0     0.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    34       1-AEIEVGR-7    
 MC  LOOP  2     0.00      0     0.0    12      26-GGG-28   
 MC  LOOP  3    17.53      5    10.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     0.00      0     0.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    53       1-AEIEVGR-7    
 ALL LOOP  2     0.00      0     0.0    12      26-GGG-28   
 ALL LOOP  3    17.53      5     5.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.00      0     0.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.882      1.000       0.500     19    25.0    76     ERRCA  
     WELL ORDERED  . . . . .   12.882      1.000       0.500     19    25.0    76     ERRCA  
     NO INTER CONTACTS . . .   12.882      1.000       0.500     19    25.0    76     ERRCA  
     SHIFTED CHAIN . . . . .   14.968      1.000       0.500     16    22.9    70     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     5     ERRCA  
     SECONDARY STRUCTURE . .    9.503      1.000       0.500     14    51.9    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   12.571      1.000       0.500      3     9.4    32     ERRCA  
     SURFACE . . . . . . . .   13.968      1.000       0.500     10    18.5    54     ERRCA  
     BURIED  . . . . . . . .   11.676      1.000       0.500      9    40.9    22     ERRCA  
     CORE  . . . . . . . . .   12.941      1.000       0.500     16    36.4    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.093      1.000       0.500     94    25.3   371     ERRMC  
     WELL ORDERED  . . . . .   13.093      1.000       0.500     94    25.3   371     ERRMC  
     NO INTER CONTACTS . . .   13.093      1.000       0.500     94    25.3   371     ERRMC  
     SHIFTED CHAIN . . . . .   15.201      1.000       0.500     79    23.2   341     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    25     ERRMC  
     SECONDARY STRUCTURE . .    9.737      1.000       0.500     69    51.9   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   12.466      1.000       0.500     14     9.1   154     ERRMC  
     SURFACE . . . . . . . .   14.092      1.000       0.500     50    18.9   264     ERRMC  
     BURIED  . . . . . . . .   11.958      1.000       0.500     44    41.1   107     ERRMC  
     CORE  . . . . . . . . .   13.202      1.000       0.500     80    36.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.035      1.000       0.500     18     6.3   284     ERRSC  
     WELL ORDERED  . . . . .   14.035      1.000       0.500     18     6.3   284     ERRSC  
     NO INTER CONTACTS . . .   14.035      1.000       0.500     18     6.3   284     ERRSC  
     RELIABLE SIDE CHAINS  .   14.035      1.000       0.500     18     7.5   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   16.240      1.000       0.500     15     5.7   262     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    25     ERRSC  
     SECONDARY STRUCTURE . .   10.602      1.000       0.500     13    13.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   16.678      1.000       0.500      2     1.8   112     ERRSC  
     SURFACE . . . . . . . .   14.655      1.000       0.500     10     4.5   222     ERRSC  
     BURIED  . . . . . . . .   13.259      1.000       0.500      8    12.9    62     ERRSC  
     CORE  . . . . . . . . .   13.704      1.000       0.500     16     9.3   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.093      1.000       0.500     94    16.0   588     ERRALL 
     WELL ORDERED  . . . . .   13.093      1.000       0.500     94    16.0   588     ERRALL 
     NO INTER CONTACTS . . .   13.093      1.000       0.500     94    16.0   588     ERRALL 
     SHIFTED CHAIN . . . . .   15.201      1.000       0.500     79    14.6   542     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    45     ERRALL 
     SECONDARY STRUCTURE . .    9.737      1.000       0.500     69    33.3   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   12.466      1.000       0.500     14     5.8   240     ERRALL 
     SURFACE . . . . . . . .   14.092      1.000       0.500     50    11.4   438     ERRALL 
     BURIED  . . . . . . . .   11.958      1.000       0.500     44    29.3   150     ERRALL 
     CORE  . . . . . . . . .   13.202      1.000       0.500     80    23.0   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)         0         4         6         7         7      19      76   DISTCA 
CA  (P)      0.00      5.26      7.89      9.21      9.21              76   DISTCA 
CA  (RMS)    0.00      1.59      1.79      2.34      2.34                   DISTCA 
 
ALL (N)         5        17        24        34        34      94     588   DISTALL 
ALL (P)      0.85      2.89      4.08      5.78      5.78             588   DISTALL 
ALL (RMS)    0.74      1.38      1.74      2.64      2.64                   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            16             3          RMSLSI 
CA  (P)       57.89         21.05          3.95          RMSLSI 
CA  (RMS)      1.67         16.42         13.90          RMSLSI 
 
 
 
END of the results output 
