 
####################################################### 
#                                                     # 
#                        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 556 atoms, 499 common with TARGET 
           Number of atoms possible to evaluate: 155 
 
 
 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 . . . . . . . . . .    84.84           31.2    64    42.7   150     ARMSMC  
     WELL ORDERED  . . . . .    84.84           31.2    64    42.7   150     ARMSMC  
     NO INTER CONTACTS . . .    84.84           31.2    64    42.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    85.47           28.6    56    40.6   138     ARMSMC  
     ALTERNATIVE PARENT  . .    42.79            0.0     1    10.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    71.32           46.7    30    55.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    85.48           20.0    15    24.2    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    91.05           30.8    39    36.8   106     ARMSMC  
     BURIED  . . . . . . . .    74.12           32.0    25    56.8    44     ARMSMC  
     CORE  . . . . . . . . .    84.64           34.7    49    55.7    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) =  -0.39252     r(1,2) =   0.44426     r(1,3) =  -0.80533 
 r(2,1) =  -0.62920     r(2,2) =   0.50894     r(2,3) =   0.58744 
 r(3,1) =   0.67084     r(3,2) =   0.73730     r(3,3) =   0.07976 
THE OFFSET VECTOR: 
 v(1) =  42.56170     v(2) =   3.98974     v(3) = -95.36509 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.62           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.53         33    43.4    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2586                            CRMSCA  
     WELL ORDERED  . . . . .    8.53         33    43.4    76     CRMSCA  
     NO INTER CONTACTS . . .    8.53         33    43.4    76     CRMSCA  
     SHIFTED CHAIN . . . . .    8.96         29    41.4    70     CRMSCA  
     ALTERNATIVE PARENT  . .    3.41          1    20.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    6.09         15    55.6    27     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   10.56          8    25.0    32     CRMSCA  
     SURFACE . . . . . . . .    9.47         20    37.0    54     CRMSCA  
     BURIED  . . . . . . . .    6.84         13    59.1    22     CRMSCA  
     CORE  . . . . . . . . .    7.77         25    56.8    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.33        155    41.8   371     CRMSMC  
     WELL ORDERED  . . . . .    8.33        155    41.8   371     CRMSMC  
     NO INTER CONTACTS . . .    8.33        155    41.8   371     CRMSMC  
     SHIFTED CHAIN . . . . .    8.64        137    40.2   341     CRMSMC  
     ALTERNATIVE PARENT  . .    3.34          5    20.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    6.31         71    53.4   133     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   10.09         36    23.4   154     CRMSMC  
     SURFACE . . . . . . . .    9.14         93    35.2   264     CRMSMC  
     BURIED  . . . . . . . .    6.93         62    57.9   107     CRMSMC  
     CORE  . . . . . . . . .    7.71        119    54.8   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    7.97         23     8.1   284     CRMSSC  
     WELL ORDERED  . . . . .    7.97         23     8.1   284     CRMSSC  
     NO INTER CONTACTS . . .    7.97         23     8.1   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    7.97         23     9.6   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    7.15         11    11.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.52          4     3.6   112     CRMSSC  
     SURFACE . . . . . . . .    8.79         13     5.9   222     CRMSSC  
     BURIED  . . . . . . . .    6.76         10    16.1    62     CRMSSC  
     CORE  . . . . . . . . .    7.85         19    11.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.33        155    26.4   588     CRMSALL 
     WELL ORDERED  . . . . .    8.33        155    26.4   588     CRMSALL 
     NO INTER CONTACTS . . .    8.33        155    26.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .    8.64        137    25.3   542     CRMSALL 
     ALTERNATIVE PARENT  . .    3.34          5    11.1    45     CRMSALL 
     SECONDARY STRUCTURE . .    6.31         71    34.3   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   10.09         36    15.0   240     CRMSALL 
     SURFACE . . . . . . . .    9.14         93    21.2   438     CRMSALL 
     BURIED  . . . . . . . .    6.93         62    41.3   150     CRMSALL 
     CORE  . . . . . . . . .    7.71        119    34.2   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.41      1    14.3     7       1-AEIEVGR-7    
 CA  LOOP  2    14.42      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     3.34      5    14.7    34       1-AEIEVGR-7    
 MC  LOOP  2    13.79     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     3.34      5     9.4    53       1-AEIEVGR-7    
 ALL LOOP  2    13.79     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 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 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 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.94     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 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.94     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 . . . . . . . . . .    7.457      1.000       0.500     33    43.4    76     ERRCA  
     WELL ORDERED  . . . . .    7.457      1.000       0.500     33    43.4    76     ERRCA  
     NO INTER CONTACTS . . .    7.457      1.000       0.500     33    43.4    76     ERRCA  
     SHIFTED CHAIN . . . . .    7.969      1.000       0.500     29    41.4    70     ERRCA  
     ALTERNATIVE PARENT  . .    3.413      1.000       0.500      1    20.0     5     ERRCA  
     SECONDARY STRUCTURE . .    5.342      1.000       0.500     15    55.6    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    9.565      1.000       0.500      8    25.0    32     ERRCA  
     SURFACE . . . . . . . .    8.498      1.000       0.500     20    37.0    54     ERRCA  
     BURIED  . . . . . . . .    5.856      1.000       0.500     13    59.1    22     ERRCA  
     CORE  . . . . . . . . .    6.783      1.000       0.500     25    56.8    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.319      1.000       0.500    155    41.8   371     ERRMC  
     WELL ORDERED  . . . . .    7.319      1.000       0.500    155    41.8   371     ERRMC  
     NO INTER CONTACTS . . .    7.319      1.000       0.500    155    41.8   371     ERRMC  
     SHIFTED CHAIN . . . . .    7.695      1.000       0.500    137    40.2   341     ERRMC  
     ALTERNATIVE PARENT  . .    2.957      1.000       0.500      5    20.0    25     ERRMC  
     SECONDARY STRUCTURE . .    5.555      1.000       0.500     71    53.4   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    9.068      1.000       0.500     36    23.4   154     ERRMC  
     SURFACE . . . . . . . .    8.206      1.000       0.500     93    35.2   264     ERRMC  
     BURIED  . . . . . . . .    5.987      1.000       0.500     62    57.9   107     ERRMC  
     CORE  . . . . . . . . .    6.789      1.000       0.500    119    54.8   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.262      1.000       0.500     23     8.1   284     ERRSC  
     WELL ORDERED  . . . . .    7.262      1.000       0.500     23     8.1   284     ERRSC  
     NO INTER CONTACTS . . .    7.262      1.000       0.500     23     8.1   284     ERRSC  
     RELIABLE SIDE CHAINS  .    7.262      1.000       0.500     23     9.6   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    7.556      1.000       0.500     21     8.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    5.730      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    6.583      1.000       0.500     11    11.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    8.023      1.000       0.500      4     3.6   112     ERRSC  
     SURFACE . . . . . . . .    8.254      1.000       0.500     13     5.9   222     ERRSC  
     BURIED  . . . . . . . .    5.973      1.000       0.500     10    16.1    62     ERRSC  
     CORE  . . . . . . . . .    7.102      1.000       0.500     19    11.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.319      1.000       0.500    155    26.4   588     ERRALL 
     WELL ORDERED  . . . . .    7.319      1.000       0.500    155    26.4   588     ERRALL 
     NO INTER CONTACTS . . .    7.319      1.000       0.500    155    26.4   588     ERRALL 
     SHIFTED CHAIN . . . . .    7.695      1.000       0.500    137    25.3   542     ERRALL 
     ALTERNATIVE PARENT  . .    2.957      1.000       0.500      5    11.1    45     ERRALL 
     SECONDARY STRUCTURE . .    5.555      1.000       0.500     71    34.3   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    9.068      1.000       0.500     36    15.0   240     ERRALL 
     SURFACE . . . . . . . .    8.206      1.000       0.500     93    21.2   438     ERRALL 
     BURIED  . . . . . . . .    5.987      1.000       0.500     62    41.3   150     ERRALL 
     CORE  . . . . . . . . .    6.789      1.000       0.500    119    34.2   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)         0         4         6        11        21      33      76   DISTCA 
CA  (P)      0.00      5.26      7.89     14.47     27.63              76   DISTCA 
CA  (RMS)    0.00      1.24      1.62      2.85      5.64                   DISTCA 
 
ALL (N)         2        20        36        50       101     155     588   DISTALL 
ALL (P)      0.34      3.40      6.12      8.50     17.18             588   DISTALL 
ALL (RMS)    0.96      1.43      1.98      2.75      5.73                   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             8          RMSLSI 
CA  (P)       57.89         32.89         10.53          RMSLSI 
CA  (RMS)      1.67          7.77         10.56          RMSLSI 
 
 
 
END of the results output 
