 
####################################################### 
#                                                     # 
#                        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 442 atoms, 385 common with TARGET 
           Number of atoms possible to evaluate: 216 
 
 
 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 . . . . . . . . . .    83.59           34.9   106    70.7   150     ARMSMC  
     WELL ORDERED  . . . . .    83.59           34.9   106    70.7   150     ARMSMC  
     NO INTER CONTACTS . . .    83.59           34.9   106    70.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    84.75           35.3   102    73.9   138     ARMSMC  
     ALTERNATIVE PARENT  . .    58.12           25.0     8    80.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    62.44           45.2    31    57.4    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    90.98           25.6    43    69.4    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    84.49           37.0    73    68.9   106     ARMSMC  
     BURIED  . . . . . . . .    81.56           30.3    33    75.0    44     ARMSMC  
     CORE  . . . . . . . . .    78.14           41.3    63    71.6    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) =   0.75366     r(1,2) =  -0.39768     r(1,3) =  -0.52331 
 r(2,1) =  -0.13310     r(2,2) =  -0.87204     r(2,3) =   0.47100 
 r(3,1) =  -0.64365     r(3,2) =  -0.28532     r(3,3) =  -0.71015 
THE OFFSET VECTOR: 
 v(1) =   2.99775     v(2) =  -3.00824     v(3) =  -1.33651 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.59           (Number of atoms:   14) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   10.61         54    71.1    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1965                            CRMSCA  
     WELL ORDERED  . . . . .   10.61         54    71.1    76     CRMSCA  
     NO INTER CONTACTS . . .   10.61         54    71.1    76     CRMSCA  
     SHIFTED CHAIN . . . . .   10.76         52    74.3    70     CRMSCA  
     ALTERNATIVE PARENT  . .    3.50          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    7.28         16    59.3    27     CRMSCA  
     SHIFTED SS UNITS  . . .    4.54          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   12.20         22    68.8    32     CRMSCA  
     SURFACE . . . . . . . .   11.45         37    68.5    54     CRMSCA  
     BURIED  . . . . . . . .    8.49         17    77.3    22     CRMSCA  
     CORE  . . . . . . . . .    9.36         32    72.7    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   10.60        216    58.2   371     CRMSMC  
     WELL ORDERED  . . . . .   10.60        216    58.2   371     CRMSMC  
     NO INTER CONTACTS . . .   10.60        216    58.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   10.74        208    61.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .    3.53         16    64.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    7.14         64    48.1   133     CRMSMC  
     SHIFTED SS UNITS  . . .    4.44         24    80.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.32         88    57.1   154     CRMSMC  
     SURFACE . . . . . . . .   11.36        148    56.1   264     CRMSMC  
     BURIED  . . . . . . . .    8.69         68    63.6   107     CRMSMC  
     CORE  . . . . . . . . .    9.23        128    59.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   284     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   284     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   112     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   222     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    62     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   10.60        216    36.7   588     CRMSALL 
     WELL ORDERED  . . . . .   10.60        216    36.7   588     CRMSALL 
     NO INTER CONTACTS . . .   10.60        216    36.7   588     CRMSALL 
     SHIFTED CHAIN . . . . .   10.74        208    38.4   542     CRMSALL 
     ALTERNATIVE PARENT  . .    3.53         16    35.6    45     CRMSALL 
     SECONDARY STRUCTURE . .    7.14         64    30.9   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.32         88    36.7   240     CRMSALL 
     SURFACE . . . . . . . .   11.36        148    33.8   438     CRMSALL 
     BURIED  . . . . . . . .    8.69         68    45.3   150     CRMSALL 
     CORE  . . . . . . . . .    9.23        128    36.8   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    14.62      3   100.0     3      26-GGG-28   
 CA  LOOP  3    14.92     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     3.59      4   100.0     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    15.07     12   100.0    12      26-GGG-28   
 MC  LOOP  3    15.11     40    80.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     3.39     16    84.2    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    15.07     12   100.0    12      26-GGG-28   
 ALL LOOP  3    15.11     40    46.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     3.39     16    45.7    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.03      3   100.0     3      26-GGG-28   
 CA  LOOP  3     2.51     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.93      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     1.42     12   100.0    12      26-GGG-28   
 MC  LOOP  3     2.29     40    80.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.16     16    84.2    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.42     12   100.0    12      26-GGG-28   
 ALL LOOP  3     2.29     40    46.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.16     16    45.7    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 . . . . . . . . . .    6.016      0.379       0.360     54    71.1    76     ERRCA  
     WELL ORDERED  . . . . .    6.016      0.379       0.360     54    71.1    76     ERRCA  
     NO INTER CONTACTS . . .    6.016      0.379       0.360     54    71.1    76     ERRCA  
     SHIFTED CHAIN . . . . .    6.071      0.382       0.360     52    74.3    70     ERRCA  
     ALTERNATIVE PARENT  . .    6.718      0.519       0.617      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .    5.727      0.423       0.432     16    59.3    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    6.699      0.395       0.369     22    68.8    32     ERRCA  
     SURFACE . . . . . . . .    5.963      0.350       0.328     37    68.5    54     ERRCA  
     BURIED  . . . . . . . .    6.131      0.441       0.429     17    77.3    22     ERRCA  
     CORE  . . . . . . . . .    5.547      0.367       0.354     32    72.7    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.011      0.375       0.364    216    58.2   371     ERRMC  
     WELL ORDERED  . . . . .    6.011      0.375       0.364    216    58.2   371     ERRMC  
     NO INTER CONTACTS . . .    6.011      0.375       0.364    216    58.2   371     ERRMC  
     SHIFTED CHAIN . . . . .    6.071      0.377       0.365    208    61.0   341     ERRMC  
     ALTERNATIVE PARENT  . .    6.748      0.526       0.608     16    64.0    25     ERRMC  
     SECONDARY STRUCTURE . .    5.619      0.411       0.436     64    48.1   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    6.810      0.398       0.368     88    57.1   154     ERRMC  
     SURFACE . . . . . . . .    5.986      0.352       0.334    148    56.1   264     ERRMC  
     BURIED  . . . . . . . .    6.064      0.425       0.431     68    63.6   107     ERRMC  
     CORE  . . . . . . . . .    5.461      0.359       0.362    128    59.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   284     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   284     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    25     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   112     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   222     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    62     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.011      0.375       0.364    216    36.7   588     ERRALL 
     WELL ORDERED  . . . . .    6.011      0.375       0.364    216    36.7   588     ERRALL 
     NO INTER CONTACTS . . .    6.011      0.375       0.364    216    36.7   588     ERRALL 
     SHIFTED CHAIN . . . . .    6.071      0.377       0.365    208    38.4   542     ERRALL 
     ALTERNATIVE PARENT  . .    6.748      0.526       0.608     16    35.6    45     ERRALL 
     SECONDARY STRUCTURE . .    5.619      0.411       0.436     64    30.9   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    6.810      0.398       0.368     88    36.7   240     ERRALL 
     SURFACE . . . . . . . .    5.986      0.352       0.334    148    33.8   438     ERRALL 
     BURIED  . . . . . . . .    6.064      0.425       0.431     68    45.3   150     ERRALL 
     CORE  . . . . . . . . .    5.461      0.359       0.362    128    36.8   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)         3        11        16        21        37      54      76   DISTCA 
CA  (P)      3.95     14.47     21.05     27.63     48.68              76   DISTCA 
CA  (RMS)    0.68      1.33      1.78      2.63      5.23                   DISTCA 
 
ALL (N)         7        35        56        91       143     216     588   DISTALL 
ALL (P)      1.19      5.95      9.52     15.48     24.32             588   DISTALL 
ALL (RMS)    0.66      1.39      1.87      2.89      4.96                   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            32            22          RMSLSI 
CA  (P)       57.89         42.11         28.95          RMSLSI 
CA  (RMS)      1.67          9.36         12.20          RMSLSI 
 
 
 
END of the results output 
