 
####################################################### 
#                                                     # 
#                        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 424 atoms, 367 common with TARGET 
           Number of atoms possible to evaluate: 357 
 
 
 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 . . . . . . . . . .    79.19           43.8   144    96.0   150     ARMSMC  
     WELL ORDERED  . . . . .    79.19           43.8   144    96.0   150     ARMSMC  
     NO INTER CONTACTS . . .    79.19           43.8   144    96.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    79.57           42.4   132    95.7   138     ARMSMC  
     ALTERNATIVE PARENT  . .    61.15           40.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    69.29           54.0    50    92.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    93.20           39.7    58    93.5    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    84.11           39.8   103    97.2   106     ARMSMC  
     BURIED  . . . . . . . .    65.24           53.7    41    93.2    44     ARMSMC  
     CORE  . . . . . . . . .    68.14           46.5    86    97.7    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) =  -0.43252     r(1,2) =   0.12988     r(1,3) =  -0.89222 
 r(2,1) =   0.62177     r(2,2) =  -0.67365     r(2,3) =  -0.39948 
 r(3,1) =  -0.65293     r(3,2) =  -0.72754     r(3,3) =   0.21062 
THE OFFSET VECTOR: 
 v(1) =  18.70366     v(2) =  22.08200     v(3) =  23.11745 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.89           (Number of atoms:   11) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   15.89         74    97.4    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2148                            CRMSCA  
     WELL ORDERED  . . . . .   15.89         74    97.4    76     CRMSCA  
     NO INTER CONTACTS . . .   15.89         74    97.4    76     CRMSCA  
     SHIFTED CHAIN . . . . .   16.34         68    97.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .   10.04          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   10.40         26    96.3    27     CRMSCA  
     SHIFTED SS UNITS  . . .   14.26          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   19.15         30    93.8    32     CRMSCA  
     SURFACE . . . . . . . .   16.22         53    98.1    54     CRMSCA  
     BURIED  . . . . . . . .   15.03         21    95.5    22     CRMSCA  
     CORE  . . . . . . . . .   13.22         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   16.03        357    96.2   371     CRMSMC  
     WELL ORDERED  . . . . .   16.03        357    96.2   371     CRMSMC  
     NO INTER CONTACTS . . .   16.03        357    96.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   16.48        327    95.9   341     CRMSMC  
     ALTERNATIVE PARENT  . .    9.57         24    96.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   10.35        126    94.7   133     CRMSMC  
     SHIFTED SS UNITS  . . .   14.38         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   19.49        142    92.2   154     CRMSMC  
     SURFACE . . . . . . . .   16.45        255    96.6   264     CRMSMC  
     BURIED  . . . . . . . .   14.94        102    95.3   107     CRMSMC  
     CORE  . . . . . . . . .   13.26        215    99.1   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   16.79         61    21.5   284     CRMSSC  
     WELL ORDERED  . . . . .   16.79         61    21.5   284     CRMSSC  
     NO INTER CONTACTS . . .   16.79         61    21.5   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   16.79         61    25.4   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    9.97         22    22.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   21.23         22    19.6   112     CRMSSC  
     SURFACE . . . . . . . .   17.44         43    19.4   222     CRMSSC  
     BURIED  . . . . . . . .   15.11         18    29.0    62     CRMSSC  
     CORE  . . . . . . . . .   13.66         39    22.7   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   16.03        357    60.7   588     CRMSALL 
     WELL ORDERED  . . . . .   16.03        357    60.7   588     CRMSALL 
     NO INTER CONTACTS . . .   16.03        357    60.7   588     CRMSALL 
     SHIFTED CHAIN . . . . .   16.48        327    60.3   542     CRMSALL 
     ALTERNATIVE PARENT  . .    9.57         24    53.3    45     CRMSALL 
     SECONDARY STRUCTURE . .   10.35        126    60.9   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   19.49        142    59.2   240     CRMSALL 
     SURFACE . . . . . . . .   16.45        255    58.2   438     CRMSALL 
     BURIED  . . . . . . . .   14.94        102    68.0   150     CRMSALL 
     CORE  . . . . . . . . .   13.26        215    61.8   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    10.18      6    85.7     7       1-AEIEVGR-7    
 CA  LOOP  2    12.89      3   100.0     3      26-GGG-28   
 CA  LOOP  3    27.59     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     4.02      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    10.29     29    85.3    34       1-AEIEVGR-7    
 MC  LOOP  2    13.68     12   100.0    12      26-GGG-28   
 MC  LOOP  3    27.57     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     4.02     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    10.29     29    54.7    53       1-AEIEVGR-7    
 ALL LOOP  2    13.68     12   100.0    12      26-GGG-28   
 ALL LOOP  3    27.57     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     4.02     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.97      6    85.7     7       1-AEIEVGR-7    
 CA  LOOP  2     0.36      3   100.0     3      26-GGG-28   
 CA  LOOP  3     4.55     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.97      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.60     29    85.3    34       1-AEIEVGR-7    
 MC  LOOP  2     1.94     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.86     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.95     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.60     29    54.7    53       1-AEIEVGR-7    
 ALL LOOP  2     1.94     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.86     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.95     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 . . . . . . . . . .   13.606      1.000       0.500     74    97.4    76     ERRCA  
     WELL ORDERED  . . . . .   13.606      1.000       0.500     74    97.4    76     ERRCA  
     NO INTER CONTACTS . . .   13.606      1.000       0.500     74    97.4    76     ERRCA  
     SHIFTED CHAIN . . . . .   14.005      1.000       0.500     68    97.1    70     ERRCA  
     ALTERNATIVE PARENT  . .    7.076      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    9.165      1.000       0.500     26    96.3    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   16.491      1.000       0.500     30    93.8    32     ERRCA  
     SURFACE . . . . . . . .   13.999      1.000       0.500     53    98.1    54     ERRCA  
     BURIED  . . . . . . . .   12.613      1.000       0.500     21    95.5    22     ERRCA  
     CORE  . . . . . . . . .   11.638      1.000       0.500     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.723      1.000       0.500    357    96.2   371     ERRMC  
     WELL ORDERED  . . . . .   13.723      1.000       0.500    357    96.2   371     ERRMC  
     NO INTER CONTACTS . . .   13.723      1.000       0.500    357    96.2   371     ERRMC  
     SHIFTED CHAIN . . . . .   14.099      1.000       0.500    327    95.9   341     ERRMC  
     ALTERNATIVE PARENT  . .    6.674      1.000       0.500     24    96.0    25     ERRMC  
     SECONDARY STRUCTURE . .    9.162      1.000       0.500    126    94.7   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   16.781      1.000       0.500    142    92.2   154     ERRMC  
     SURFACE . . . . . . . .   14.167      1.000       0.500    255    96.6   264     ERRMC  
     BURIED  . . . . . . . .   12.613      1.000       0.500    102    95.3   107     ERRMC  
     CORE  . . . . . . . . .   11.702      1.000       0.500    215    99.1   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.519      1.000       0.500     61    21.5   284     ERRSC  
     WELL ORDERED  . . . . .   14.519      1.000       0.500     61    21.5   284     ERRSC  
     NO INTER CONTACTS . . .   14.519      1.000       0.500     61    21.5   284     ERRSC  
     RELIABLE SIDE CHAINS  .   14.519      1.000       0.500     61    25.4   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   14.984      1.000       0.500     55    21.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    5.101      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .    8.869      1.000       0.500     22    22.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   18.989      1.000       0.500     22    19.6   112     ERRSC  
     SURFACE . . . . . . . .   15.314      1.000       0.500     43    19.4   222     ERRSC  
     BURIED  . . . . . . . .   12.619      1.000       0.500     18    29.0    62     ERRSC  
     CORE  . . . . . . . . .   11.997      1.000       0.500     39    22.7   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.723      1.000       0.500    357    60.7   588     ERRALL 
     WELL ORDERED  . . . . .   13.723      1.000       0.500    357    60.7   588     ERRALL 
     NO INTER CONTACTS . . .   13.723      1.000       0.500    357    60.7   588     ERRALL 
     SHIFTED CHAIN . . . . .   14.099      1.000       0.500    327    60.3   542     ERRALL 
     ALTERNATIVE PARENT  . .    6.674      1.000       0.500     24    53.3    45     ERRALL 
     SECONDARY STRUCTURE . .    9.162      1.000       0.500    126    60.9   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   16.781      1.000       0.500    142    59.2   240     ERRALL 
     SURFACE . . . . . . . .   14.167      1.000       0.500    255    58.2   438     ERRALL 
     BURIED  . . . . . . . .   12.613      1.000       0.500    102    68.0   150     ERRALL 
     CORE  . . . . . . . . .   11.702      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)         2         5        11        13        28      74      76   DISTCA 
CA  (P)      2.63      6.58     14.47     17.11     36.84              76   DISTCA 
CA  (RMS)    0.85      1.29      1.89      2.49      5.84                   DISTCA 
 
ALL (N)         9        29        44        65       136     357     588   DISTALL 
ALL (P)      1.53      4.93      7.48     11.05     23.13             588   DISTALL 
ALL (RMS)    0.71      1.35      1.74      2.72      5.91                   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            30          RMSLSI 
CA  (P)       57.89         57.89         39.47          RMSLSI 
CA  (RMS)      1.67         13.22         19.15          RMSLSI 
 
 
 
END of the results output 
