 
####################################################### 
#                                                     # 
#                        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 519 atoms, 473 common with TARGET 
           Number of atoms possible to evaluate: 199 
 
 
 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 . . . . . . . . . .    96.00           32.5    80    53.3   150     ARMSMC  
     WELL ORDERED  . . . . .    96.00           32.5    80    53.3   150     ARMSMC  
     NO INTER CONTACTS . . .    96.00           32.5    80    53.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .   100.95           30.0    70    50.7   138     ARMSMC  
     ALTERNATIVE PARENT  . .    99.97           33.3     3    30.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    80.39           36.8    38    70.4    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   106.24           30.8    26    41.9    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    95.79           30.2    53    50.0   106     ARMSMC  
     BURIED  . . . . . . . .    96.41           37.0    27    61.4    44     ARMSMC  
     CORE  . . . . . . . . .    90.66           33.3    54    61.4    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) =  -0.10223     r(1,2) =  -0.88474     r(1,3) =  -0.45473 
 r(2,1) =   0.14659     r(2,2) =   0.43874     r(2,3) =  -0.88658 
 r(3,1) =   0.98390     r(3,2) =  -0.15729     r(3,3) =   0.08484 
THE OFFSET VECTOR: 
 v(1) =   9.36670     v(2) =   1.41804     v(3) = -35.10330 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   2.00           (Number of atoms:    5) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.20         42    55.3    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3381                            CRMSCA  
     WELL ORDERED  . . . . .   14.20         42    55.3    76     CRMSCA  
     NO INTER CONTACTS . . .   14.20         42    55.3    76     CRMSCA  
     SHIFTED CHAIN . . . . .   14.87         37    52.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .   10.84          2    40.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   10.01         19    70.4    27     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   16.16         14    43.8    32     CRMSCA  
     SURFACE . . . . . . . .   14.55         28    51.9    54     CRMSCA  
     BURIED  . . . . . . . .   13.49         14    63.6    22     CRMSCA  
     CORE  . . . . . . . . .   13.11         28    63.6    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.19        199    53.6   371     CRMSMC  
     WELL ORDERED  . . . . .   14.19        199    53.6   371     CRMSMC  
     NO INTER CONTACTS . . .   14.19        199    53.6   371     CRMSMC  
     SHIFTED CHAIN . . . . .   14.84        175    51.3   341     CRMSMC  
     ALTERNATIVE PARENT  . .   10.96          9    36.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   10.30         90    67.7   133     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   16.03         63    40.9   154     CRMSMC  
     SURFACE . . . . . . . .   14.52        134    50.8   264     CRMSMC  
     BURIED  . . . . . . . .   13.49         65    60.7   107     CRMSMC  
     CORE  . . . . . . . . .   13.26        136    62.7   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.61         31    10.9   284     CRMSSC  
     WELL ORDERED  . . . . .   13.61         31    10.9   284     CRMSSC  
     NO INTER CONTACTS . . .   13.61         31    10.9   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.61         31    12.9   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   10.17         14    14.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   13.73          7     6.2   112     CRMSSC  
     SURFACE . . . . . . . .   13.50         22     9.9   222     CRMSSC  
     BURIED  . . . . . . . .   13.90          9    14.5    62     CRMSSC  
     CORE  . . . . . . . . .   13.58         24    14.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.19        199    33.8   588     CRMSALL 
     WELL ORDERED  . . . . .   14.19        199    33.8   588     CRMSALL 
     NO INTER CONTACTS . . .   14.19        199    33.8   588     CRMSALL 
     SHIFTED CHAIN . . . . .   14.84        175    32.3   542     CRMSALL 
     ALTERNATIVE PARENT  . .   10.96          9    20.0    45     CRMSALL 
     SECONDARY STRUCTURE . .   10.30         90    43.5   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   16.03         63    26.2   240     CRMSALL 
     SURFACE . . . . . . . .   14.52        134    30.6   438     CRMSALL 
     BURIED  . . . . . . . .   13.49         65    43.3   150     CRMSALL 
     CORE  . . . . . . . . .   13.26        136    39.1   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     7.03      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2    25.01      3   100.0     3      26-GGG-28   
 CA  LOOP  3     0.00      0     0.0    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     7.15     23    67.6    34       1-AEIEVGR-7    
 MC  LOOP  2    25.26     12   100.0    12      26-GGG-28   
 MC  LOOP  3     0.00      0     0.0    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     7.15     23    43.4    53       1-AEIEVGR-7    
 ALL LOOP  2    25.26     12   100.0    12      26-GGG-28   
 ALL LOOP  3     0.00      0     0.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.00      0     0.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.07      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2     0.09      3   100.0     3      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.43     23    67.6    34       1-AEIEVGR-7    
 MC  LOOP  2     1.76     12   100.0    12      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.43     23    43.4    53       1-AEIEVGR-7    
 ALL LOOP  2     1.76     12   100.0    12      26-GGG-28   
 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 . . . . . . . . . .   12.177      1.000       0.500     42    55.3    76     ERRCA  
     WELL ORDERED  . . . . .   12.177      1.000       0.500     42    55.3    76     ERRCA  
     NO INTER CONTACTS . . .   12.177      1.000       0.500     42    55.3    76     ERRCA  
     SHIFTED CHAIN . . . . .   13.033      1.000       0.500     37    52.9    70     ERRCA  
     ALTERNATIVE PARENT  . .    9.597      1.000       0.500      2    40.0     5     ERRCA  
     SECONDARY STRUCTURE . .    8.673      1.000       0.500     19    70.4    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   14.107      1.000       0.500     14    43.8    32     ERRCA  
     SURFACE . . . . . . . .   12.127      1.000       0.500     28    51.9    54     ERRCA  
     BURIED  . . . . . . . .   12.276      1.000       0.500     14    63.6    22     ERRCA  
     CORE  . . . . . . . . .   11.212      1.000       0.500     28    63.6    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.259      1.000       0.500    199    53.6   371     ERRMC  
     WELL ORDERED  . . . . .   12.259      1.000       0.500    199    53.6   371     ERRMC  
     NO INTER CONTACTS . . .   12.259      1.000       0.500    199    53.6   371     ERRMC  
     SHIFTED CHAIN . . . . .   13.087      1.000       0.500    175    51.3   341     ERRMC  
     ALTERNATIVE PARENT  . .    9.902      1.000       0.500      9    36.0    25     ERRMC  
     SECONDARY STRUCTURE . .    9.010      1.000       0.500     90    67.7   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   13.981      1.000       0.500     63    40.9   154     ERRMC  
     SURFACE . . . . . . . .   12.212      1.000       0.500    134    50.8   264     ERRMC  
     BURIED  . . . . . . . .   12.355      1.000       0.500     65    60.7   107     ERRMC  
     CORE  . . . . . . . . .   11.461      1.000       0.500    136    62.7   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.038      1.000       0.500     31    10.9   284     ERRSC  
     WELL ORDERED  . . . . .   12.038      1.000       0.500     31    10.9   284     ERRSC  
     NO INTER CONTACTS . . .   12.038      1.000       0.500     31    10.9   284     ERRSC  
     RELIABLE SIDE CHAINS  .   12.038      1.000       0.500     31    12.9   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   12.687      1.000       0.500     27    10.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   16.219      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    9.261      1.000       0.500     14    14.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.515      1.000       0.500      7     6.2   112     ERRSC  
     SURFACE . . . . . . . .   11.678      1.000       0.500     22     9.9   222     ERRSC  
     BURIED  . . . . . . . .   12.919      1.000       0.500      9    14.5    62     ERRSC  
     CORE  . . . . . . . . .   11.899      1.000       0.500     24    14.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.259      1.000       0.500    199    33.8   588     ERRALL 
     WELL ORDERED  . . . . .   12.259      1.000       0.500    199    33.8   588     ERRALL 
     NO INTER CONTACTS . . .   12.259      1.000       0.500    199    33.8   588     ERRALL 
     SHIFTED CHAIN . . . . .   13.087      1.000       0.500    175    32.3   542     ERRALL 
     ALTERNATIVE PARENT  . .    9.902      1.000       0.500      9    20.0    45     ERRALL 
     SECONDARY STRUCTURE . .    9.010      1.000       0.500     90    43.5   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   13.981      1.000       0.500     63    26.2   240     ERRALL 
     SURFACE . . . . . . . .   12.212      1.000       0.500    134    30.6   438     ERRALL 
     BURIED  . . . . . . . .   12.355      1.000       0.500     65    43.3   150     ERRALL 
     CORE  . . . . . . . . .   11.461      1.000       0.500    136    39.1   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         2         5         9        18      42      76   DISTCA 
CA  (P)      1.32      2.63      6.58     11.84     23.68              76   DISTCA 
CA  (RMS)    0.82      1.48      2.00      3.37      5.80                   DISTCA 
 
ALL (N)         1         6        19        39        85     199     588   DISTALL 
ALL (P)      0.17      1.02      3.23      6.63     14.46             588   DISTALL 
ALL (RMS)    0.82      1.66      2.25      3.45      5.95                   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            28            14          RMSLSI 
CA  (P)       57.89         36.84         18.42          RMSLSI 
CA  (RMS)      1.67         13.11         16.16          RMSLSI 
 
 
 
END of the results output 
