 
####################################################### 
#                                                     # 
#                        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 482 atoms, 425 common with TARGET 
           Number of atoms possible to evaluate: 273 
 
 
 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 . . . . . . . . . .   106.29           23.6   110    73.3   150     ARMSMC  
     WELL ORDERED  . . . . .   106.29           23.6   110    73.3   150     ARMSMC  
     NO INTER CONTACTS . . .   106.29           23.6   110    73.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .   107.08           24.8   101    73.2   138     ARMSMC  
     ALTERNATIVE PARENT  . .    87.76           66.7     6    60.0    10     ARMSMC  
     SECONDARY STRUCTURE . .   111.04           19.6    46    85.2    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   103.22           32.6    43    69.4    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .   105.72           30.6    72    67.9   106     ARMSMC  
     BURIED  . . . . . . . .   107.37           10.5    38    86.4    44     ARMSMC  
     CORE  . . . . . . . . .   108.22           17.9    67    76.1    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) =  -0.28982     r(1,2) =  -0.13689     r(1,3) =   0.94724 
 r(2,1) =  -0.77786     r(2,2) =  -0.54294     r(2,3) =  -0.31646 
 r(3,1) =   0.55762     r(3,2) =  -0.82854     r(3,3) =   0.05087 
THE OFFSET VECTOR: 
 v(1) =  33.59762     v(2) = 139.34467     v(3) =   9.69865 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.47           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.69         57    75.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2577                            CRMSCA  
     WELL ORDERED  . . . . .   14.69         57    75.0    76     CRMSCA  
     NO INTER CONTACTS . . .   14.69         57    75.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .   14.30         52    74.3    70     CRMSCA  
     ALTERNATIVE PARENT  . .   20.56          3    60.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   19.43         23    85.2    27     CRMSCA  
     SHIFTED SS UNITS  . . .   16.26          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   12.88         22    68.8    32     CRMSCA  
     SURFACE . . . . . . . .   13.82         38    70.4    54     CRMSCA  
     BURIED  . . . . . . . .   16.28         19    86.4    22     CRMSCA  
     CORE  . . . . . . . . .   15.72         35    79.5    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.66        273    73.6   371     CRMSMC  
     WELL ORDERED  . . . . .   14.66        273    73.6   371     CRMSMC  
     NO INTER CONTACTS . . .   14.66        273    73.6   371     CRMSMC  
     SHIFTED CHAIN . . . . .   14.22        249    73.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .   20.75         15    60.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   19.15        111    83.5   133     CRMSMC  
     SHIFTED SS UNITS  . . .   16.77         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.75        102    66.2   154     CRMSMC  
     SURFACE . . . . . . . .   14.17        182    68.9   264     CRMSMC  
     BURIED  . . . . . . . .   15.60         91    85.0   107     CRMSMC  
     CORE  . . . . . . . . .   15.70        171    78.8   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   14.65         45    15.8   284     CRMSSC  
     WELL ORDERED  . . . . .   14.65         45    15.8   284     CRMSSC  
     NO INTER CONTACTS . . .   14.65         45    15.8   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.65         45    18.8   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   17.67         19    19.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   12.59         14    12.5   112     CRMSSC  
     SURFACE . . . . . . . .   15.62         30    13.5   222     CRMSSC  
     BURIED  . . . . . . . .   12.49         15    24.2    62     CRMSSC  
     CORE  . . . . . . . . .   15.50         31    18.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.66        273    46.4   588     CRMSALL 
     WELL ORDERED  . . . . .   14.66        273    46.4   588     CRMSALL 
     NO INTER CONTACTS . . .   14.66        273    46.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .   14.22        249    45.9   542     CRMSALL 
     ALTERNATIVE PARENT  . .   20.75         15    33.3    45     CRMSALL 
     SECONDARY STRUCTURE . .   19.15        111    53.6   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.75        102    42.5   240     CRMSALL 
     SURFACE . . . . . . . .   14.17        182    41.6   438     CRMSALL 
     BURIED  . . . . . . . .   15.60         91    60.7   150     CRMSALL 
     CORE  . . . . . . . . .   15.70        171    49.1   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    13.54      3    42.9     7       1-AEIEVGR-7    
 CA  LOOP  2     5.87      3   100.0     3      26-GGG-28   
 CA  LOOP  3     7.36     10   100.0    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    13.57     14    41.2    34       1-AEIEVGR-7    
 MC  LOOP  2     5.84     12   100.0    12      26-GGG-28   
 MC  LOOP  3     7.43     48    96.0    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    13.57     14    26.4    53       1-AEIEVGR-7    
 ALL LOOP  2     5.84     12   100.0    12      26-GGG-28   
 ALL LOOP  3     7.43     48    55.2    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     0.30      3    42.9     7       1-AEIEVGR-7    
 CA  LOOP  2     0.05      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.88     10   100.0    10      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.71     14    41.2    34       1-AEIEVGR-7    
 MC  LOOP  2     1.83     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.14     48    96.0    50      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.71     14    26.4    53       1-AEIEVGR-7    
 ALL LOOP  2     1.83     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.14     48    55.2    87      40-DKRVEKVTDY-49   
 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 . . . . . . . . . .   12.063      1.000       0.500     57    75.0    76     ERRCA  
     WELL ORDERED  . . . . .   12.063      1.000       0.500     57    75.0    76     ERRCA  
     NO INTER CONTACTS . . .   12.063      1.000       0.500     57    75.0    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.548      1.000       0.500     52    74.3    70     ERRCA  
     ALTERNATIVE PARENT  . .   20.163      1.000       0.500      3    60.0     5     ERRCA  
     SECONDARY STRUCTURE . .   17.989      1.000       0.500     23    85.2    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   10.313      1.000       0.500     22    68.8    32     ERRCA  
     SURFACE . . . . . . . .   11.393      1.000       0.500     38    70.4    54     ERRCA  
     BURIED  . . . . . . . .   13.405      1.000       0.500     19    86.4    22     ERRCA  
     CORE  . . . . . . . . .   13.163      1.000       0.500     35    79.5    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.173      1.000       0.500    273    73.6   371     ERRMC  
     WELL ORDERED  . . . . .   12.173      1.000       0.500    273    73.6   371     ERRMC  
     NO INTER CONTACTS . . .   12.173      1.000       0.500    273    73.6   371     ERRMC  
     SHIFTED CHAIN . . . . .   11.632      1.000       0.500    249    73.0   341     ERRMC  
     ALTERNATIVE PARENT  . .   20.210      1.000       0.500     15    60.0    25     ERRMC  
     SECONDARY STRUCTURE . .   17.830      1.000       0.500    111    83.5   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.302      1.000       0.500    102    66.2   154     ERRMC  
     SURFACE . . . . . . . .   11.785      1.000       0.500    182    68.9   264     ERRMC  
     BURIED  . . . . . . . .   12.951      1.000       0.500     91    85.0   107     ERRMC  
     CORE  . . . . . . . . .   13.290      1.000       0.500    171    78.8   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.014      1.000       0.500     45    15.8   284     ERRSC  
     WELL ORDERED  . . . . .   13.014      1.000       0.500     45    15.8   284     ERRSC  
     NO INTER CONTACTS . . .   13.014      1.000       0.500     45    15.8   284     ERRSC  
     RELIABLE SIDE CHAINS  .   13.014      1.000       0.500     45    18.8   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   12.475      1.000       0.500     41    15.6   262     ERRSC  
     ALTERNATIVE PARENT  . .   20.050      1.000       0.500      3    12.0    25     ERRSC  
     SECONDARY STRUCTURE . .   16.831      1.000       0.500     19    19.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   11.418      1.000       0.500     14    12.5   112     ERRSC  
     SURFACE . . . . . . . .   13.711      1.000       0.500     30    13.5   222     ERRSC  
     BURIED  . . . . . . . .   11.620      1.000       0.500     15    24.2    62     ERRSC  
     CORE  . . . . . . . . .   13.735      1.000       0.500     31    18.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.173      1.000       0.500    273    46.4   588     ERRALL 
     WELL ORDERED  . . . . .   12.173      1.000       0.500    273    46.4   588     ERRALL 
     NO INTER CONTACTS . . .   12.173      1.000       0.500    273    46.4   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.632      1.000       0.500    249    45.9   542     ERRALL 
     ALTERNATIVE PARENT  . .   20.210      1.000       0.500     15    33.3    45     ERRALL 
     SECONDARY STRUCTURE . .   17.830      1.000       0.500    111    53.6   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.302      1.000       0.500    102    42.5   240     ERRALL 
     SURFACE . . . . . . . .   11.785      1.000       0.500    182    41.6   438     ERRALL 
     BURIED  . . . . . . . .   12.951      1.000       0.500     91    60.7   150     ERRALL 
     CORE  . . . . . . . . .   13.290      1.000       0.500    171    49.1   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         5         6        12        26      57      76   DISTCA 
CA  (P)      1.32      6.58      7.89     15.79     34.21              76   DISTCA 
CA  (RMS)    0.57      1.27      1.47      3.14      5.59                   DISTCA 
 
ALL (N)         3        17        29        55       120     273     588   DISTALL 
ALL (P)      0.51      2.89      4.93      9.35     20.41             588   DISTALL 
ALL (RMS)    0.67      1.47      2.03      3.13      5.59                   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            35            22          RMSLSI 
CA  (P)       57.89         46.05         28.95          RMSLSI 
CA  (RMS)      1.67         15.72         12.88          RMSLSI 
 
 
 
END of the results output 
