 
####################################################### 
#                                                     # 
#                        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 521 atoms, 464 common with TARGET 
           Number of atoms possible to evaluate: 208 
 
 
 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 . . . . . . . . . .    84.45           36.0    86    57.3   150     ARMSMC  
     WELL ORDERED  . . . . .    84.45           36.0    86    57.3   150     ARMSMC  
     NO INTER CONTACTS . . .    84.45           36.0    86    57.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    80.99           35.9    78    56.5   138     ARMSMC  
     ALTERNATIVE PARENT  . .    23.10           50.0     2    20.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    84.83           30.0    30    55.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    73.70           52.8    36    58.1    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    91.82           36.8    57    53.8   106     ARMSMC  
     BURIED  . . . . . . . .    67.64           34.5    29    65.9    44     ARMSMC  
     CORE  . . . . . . . . .    91.40           24.0    50    56.8    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) =   0.28961     r(1,2) =  -0.92953     r(1,3) =  -0.22827 
 r(2,1) =  -0.69825     r(2,2) =  -0.04206     r(2,3) =  -0.71462 
 r(3,1) =   0.65465     r(3,2) =   0.36635     r(3,3) =  -0.66122 
THE OFFSET VECTOR: 
 v(1) =  -5.49497     v(2) =   6.49936     v(3) =   0.13343 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.54           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.68         44    57.9    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3337                            CRMSCA  
     WELL ORDERED  . . . . .   14.68         44    57.9    76     CRMSCA  
     NO INTER CONTACTS . . .   14.68         44    57.9    76     CRMSCA  
     SHIFTED CHAIN . . . . .   15.34         40    57.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .   25.57          1    20.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    7.48         15    55.6    27     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   20.63         19    59.4    32     CRMSCA  
     SURFACE . . . . . . . .   16.72         29    53.7    54     CRMSCA  
     BURIED  . . . . . . . .    9.59         15    68.2    22     CRMSCA  
     CORE  . . . . . . . . .    7.49         25    56.8    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.85        208    56.1   371     CRMSMC  
     WELL ORDERED  . . . . .   14.85        208    56.1   371     CRMSMC  
     NO INTER CONTACTS . . .   14.85        208    56.1   371     CRMSMC  
     SHIFTED CHAIN . . . . .   15.51        189    55.4   341     CRMSMC  
     ALTERNATIVE PARENT  . .   24.97          5    20.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    7.64         72    54.1   133     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   20.84         90    58.4   154     CRMSMC  
     SURFACE . . . . . . . .   16.89        137    51.9   264     CRMSMC  
     BURIED  . . . . . . . .    9.78         71    66.4   107     CRMSMC  
     CORE  . . . . . . . . .    7.58        118    54.4   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   16.32         32    11.3   284     CRMSSC  
     WELL ORDERED  . . . . .   16.32         32    11.3   284     CRMSSC  
     NO INTER CONTACTS . . .   16.32         32    11.3   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   16.32         32    13.3   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    8.86         12    12.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   22.70         14    12.5   112     CRMSSC  
     SURFACE . . . . . . . .   18.62         21     9.5   222     CRMSSC  
     BURIED  . . . . . . . .   10.65         11    17.7    62     CRMSSC  
     CORE  . . . . . . . . .    8.54         18    10.5   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.85        208    35.4   588     CRMSALL 
     WELL ORDERED  . . . . .   14.85        208    35.4   588     CRMSALL 
     NO INTER CONTACTS . . .   14.85        208    35.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .   15.51        189    34.9   542     CRMSALL 
     ALTERNATIVE PARENT  . .   24.97          5    11.1    45     CRMSALL 
     SECONDARY STRUCTURE . .    7.64         72    34.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   20.84         90    37.5   240     CRMSALL 
     SURFACE . . . . . . . .   16.89        137    31.3   438     CRMSALL 
     BURIED  . . . . . . . .    9.78         71    47.3   150     CRMSALL 
     CORE  . . . . . . . . .    7.58        118    33.9   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    32.07      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2     2.98      3   100.0     3      26-GGG-28   
 CA  LOOP  3    19.67      7    70.0    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    31.80     24    70.6    34       1-AEIEVGR-7    
 MC  LOOP  2     2.99     12   100.0    12      26-GGG-28   
 MC  LOOP  3    19.71     35    70.0    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    31.80     24    45.3    53       1-AEIEVGR-7    
 ALL LOOP  2     2.99     12   100.0    12      26-GGG-28   
 ALL LOOP  3    19.71     35    40.2    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     2.47      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2     0.10      3   100.0     3      26-GGG-28   
 CA  LOOP  3     1.57      7    70.0    10      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.15     24    70.6    34       1-AEIEVGR-7    
 MC  LOOP  2     1.37     12   100.0    12      26-GGG-28   
 MC  LOOP  3     1.82     35    70.0    50      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.15     24    45.3    53       1-AEIEVGR-7    
 ALL LOOP  2     1.37     12   100.0    12      26-GGG-28   
 ALL LOOP  3     1.82     35    40.2    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 . . . . . . . . . .   11.003      1.000       0.500     44    57.9    76     ERRCA  
     WELL ORDERED  . . . . .   11.003      1.000       0.500     44    57.9    76     ERRCA  
     NO INTER CONTACTS . . .   11.003      1.000       0.500     44    57.9    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.710      1.000       0.500     40    57.1    70     ERRCA  
     ALTERNATIVE PARENT  . .   25.572      1.000       0.500      1    20.0     5     ERRCA  
     SECONDARY STRUCTURE . .    5.489      1.000       0.500     15    55.6    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   17.311      1.000       0.500     19    59.4    32     ERRCA  
     SURFACE . . . . . . . .   12.950      1.000       0.500     29    53.7    54     ERRCA  
     BURIED  . . . . . . . .    7.238      1.000       0.500     15    68.2    22     ERRCA  
     CORE  . . . . . . . . .    6.209      1.000       0.500     25    56.8    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.301      1.000       0.500    208    56.1   371     ERRMC  
     WELL ORDERED  . . . . .   11.301      1.000       0.500    208    56.1   371     ERRMC  
     NO INTER CONTACTS . . .   11.301      1.000       0.500    208    56.1   371     ERRMC  
     SHIFTED CHAIN . . . . .   12.022      1.000       0.500    189    55.4   341     ERRMC  
     ALTERNATIVE PARENT  . .   24.920      1.000       0.500      5    20.0    25     ERRMC  
     SECONDARY STRUCTURE . .    5.799      1.000       0.500     72    54.1   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   17.774      1.000       0.500     90    58.4   154     ERRMC  
     SURFACE . . . . . . . .   13.260      1.000       0.500    137    51.9   264     ERRMC  
     BURIED  . . . . . . . .    7.522      1.000       0.500     71    66.4   107     ERRMC  
     CORE  . . . . . . . . .    6.364      1.000       0.500    118    54.4   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.268      1.000       0.500     32    11.3   284     ERRSC  
     WELL ORDERED  . . . . .   13.268      1.000       0.500     32    11.3   284     ERRSC  
     NO INTER CONTACTS . . .   13.268      1.000       0.500     32    11.3   284     ERRSC  
     RELIABLE SIDE CHAINS  .   13.268      1.000       0.500     32    13.3   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   14.095      1.000       0.500     29    11.1   262     ERRSC  
     ALTERNATIVE PARENT  . .   24.970      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    7.333      1.000       0.500     12    12.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   20.778      1.000       0.500     14    12.5   112     ERRSC  
     SURFACE . . . . . . . .   15.856      1.000       0.500     21     9.5   222     ERRSC  
     BURIED  . . . . . . . .    8.328      1.000       0.500     11    17.7    62     ERRSC  
     CORE  . . . . . . . . .    7.427      1.000       0.500     18    10.5   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.301      1.000       0.500    208    35.4   588     ERRALL 
     WELL ORDERED  . . . . .   11.301      1.000       0.500    208    35.4   588     ERRALL 
     NO INTER CONTACTS . . .   11.301      1.000       0.500    208    35.4   588     ERRALL 
     SHIFTED CHAIN . . . . .   12.022      1.000       0.500    189    34.9   542     ERRALL 
     ALTERNATIVE PARENT  . .   24.920      1.000       0.500      5    11.1    45     ERRALL 
     SECONDARY STRUCTURE . .    5.799      1.000       0.500     72    34.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   17.774      1.000       0.500     90    37.5   240     ERRALL 
     SURFACE . . . . . . . .   13.260      1.000       0.500    137    31.3   438     ERRALL 
     BURIED  . . . . . . . .    7.522      1.000       0.500     71    47.3   150     ERRALL 
     CORE  . . . . . . . . .    6.364      1.000       0.500    118    33.9   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         7        16        29      44      76   DISTCA 
CA  (P)      1.32      6.58      9.21     21.05     38.16              76   DISTCA 
CA  (RMS)    0.87      1.32      1.81      3.05      5.63                   DISTCA 
 
ALL (N)         3        19        35        70       129     208     588   DISTALL 
ALL (P)      0.51      3.23      5.95     11.90     21.94             588   DISTALL 
ALL (RMS)    0.93      1.54      2.05      3.20      5.49                   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            25            19          RMSLSI 
CA  (P)       57.89         32.89         25.00          RMSLSI 
CA  (RMS)      1.67          7.49         20.63          RMSLSI 
 
 
 
END of the results output 
