 
####################################################### 
#                                                     # 
#                        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 567 atoms, 510 common with TARGET 
           Number of atoms possible to evaluate: 126 
 
 
 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 . . . . . . . . . .    69.57           40.0    40    26.7   150     ARMSMC  
     WELL ORDERED  . . . . .    69.57           40.0    40    26.7   150     ARMSMC  
     NO INTER CONTACTS . . .    69.57           40.0    40    26.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    70.02           35.3    34    24.6   138     ARMSMC  
     ALTERNATIVE PARENT  . .    61.58            0.0     1    10.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    56.03           48.3    29    53.7    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    78.83           28.6     7    11.3    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    76.05           50.0    22    20.8   106     ARMSMC  
     BURIED  . . . . . . . .    60.72           27.8    18    40.9    44     ARMSMC  
     CORE  . . . . . . . . .    67.45           42.4    33    37.5    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) =  -0.35703     r(1,2) =   0.00815     r(1,3) =   0.93406 
 r(2,1) =   0.80197     r(2,2) =   0.51537     r(2,3) =   0.30205 
 r(3,1) =  -0.47892     r(3,2) =   0.85693     r(3,3) =  -0.19053 
THE OFFSET VECTOR: 
 v(1) = -31.83056     v(2) = -10.70712     v(3) = -16.60596 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.37           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.36         26    34.2    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3598                            CRMSCA  
     WELL ORDERED  . . . . .    9.36         26    34.2    76     CRMSCA  
     NO INTER CONTACTS . . .    9.36         26    34.2    76     CRMSCA  
     SHIFTED CHAIN . . . . .    9.19         23    32.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .    0.58          1    20.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    8.62         18    66.7    27     CRMSCA  
     SHIFTED SS UNITS  . . .    3.11          5    83.3     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   10.08          5    15.6    32     CRMSCA  
     SURFACE . . . . . . . .   10.69         15    27.8    54     CRMSCA  
     BURIED  . . . . . . . .    7.15         11    50.0    22     CRMSCA  
     CORE  . . . . . . . . .    9.18         21    47.7    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.32        126    34.0   371     CRMSMC  
     WELL ORDERED  . . . . .    9.32        126    34.0   371     CRMSMC  
     NO INTER CONTACTS . . .    9.32        126    34.0   371     CRMSMC  
     SHIFTED CHAIN . . . . .    9.07        111    32.6   341     CRMSMC  
     ALTERNATIVE PARENT  . .    0.77          5    20.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    8.61         87    65.4   133     CRMSMC  
     SHIFTED SS UNITS  . . .    3.17         24    80.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   10.27         24    15.6   154     CRMSMC  
     SURFACE . . . . . . . .   10.47         72    27.3   264     CRMSMC  
     BURIED  . . . . . . . .    7.52         54    50.5   107     CRMSMC  
     CORE  . . . . . . . . .    9.08        102    47.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.43         22     7.7   284     CRMSSC  
     WELL ORDERED  . . . . .    8.43         22     7.7   284     CRMSSC  
     NO INTER CONTACTS . . .    8.43         22     7.7   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.43         22     9.2   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    7.89         15    15.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.85          4     3.6   112     CRMSSC  
     SURFACE . . . . . . . .    9.11         12     5.4   222     CRMSSC  
     BURIED  . . . . . . . .    7.54         10    16.1    62     CRMSSC  
     CORE  . . . . . . . . .    7.79         18    10.5   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.32        126    21.4   588     CRMSALL 
     WELL ORDERED  . . . . .    9.32        126    21.4   588     CRMSALL 
     NO INTER CONTACTS . . .    9.32        126    21.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .    9.07        111    20.5   542     CRMSALL 
     ALTERNATIVE PARENT  . .    0.77          5    11.1    45     CRMSALL 
     SECONDARY STRUCTURE . .    8.61         87    42.0   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   10.27         24    10.0   240     CRMSALL 
     SURFACE . . . . . . . .   10.47         72    16.4   438     CRMSALL 
     BURIED  . . . . . . . .    7.52         54    36.0   150     CRMSALL 
     CORE  . . . . . . . . .    9.08        102    29.3   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     0.00      0     0.0     3      26-GGG-28   
 CA  LOOP  3    15.33      1    10.0    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     0.00      0     0.0    34       1-AEIEVGR-7    
 MC  LOOP  2     0.00      0     0.0    12      26-GGG-28   
 MC  LOOP  3    15.37      5    10.0    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     0.00      0     0.0    53       1-AEIEVGR-7    
 ALL LOOP  2     0.00      0     0.0    12      26-GGG-28   
 ALL LOOP  3    15.37      5     5.7    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). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 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). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 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). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 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 . . . . . . . . . .    7.421      1.000       0.500     26    34.2    76     ERRCA  
     WELL ORDERED  . . . . .    7.421      1.000       0.500     26    34.2    76     ERRCA  
     NO INTER CONTACTS . . .    7.421      1.000       0.500     26    34.2    76     ERRCA  
     SHIFTED CHAIN . . . . .    7.094      1.000       0.500     23    32.9    70     ERRCA  
     ALTERNATIVE PARENT  . .    0.579      1.000       0.500      1    20.0     5     ERRCA  
     SECONDARY STRUCTURE . .    6.660      1.000       0.500     18    66.7    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    8.853      1.000       0.500      5    15.6    32     ERRCA  
     SURFACE . . . . . . . .    8.715      1.000       0.500     15    27.8    54     ERRCA  
     BURIED  . . . . . . . .    5.657      1.000       0.500     11    50.0    22     ERRCA  
     CORE  . . . . . . . . .    7.080      1.000       0.500     21    47.7    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.471      1.000       0.500    126    34.0   371     ERRMC  
     WELL ORDERED  . . . . .    7.471      1.000       0.500    126    34.0   371     ERRMC  
     NO INTER CONTACTS . . .    7.471      1.000       0.500    126    34.0   371     ERRMC  
     SHIFTED CHAIN . . . . .    7.098      1.000       0.500    111    32.6   341     ERRMC  
     ALTERNATIVE PARENT  . .    0.740      1.000       0.500      5    20.0    25     ERRMC  
     SECONDARY STRUCTURE . .    6.735      1.000       0.500     87    65.4   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    9.140      1.000       0.500     24    15.6   154     ERRMC  
     SURFACE . . . . . . . .    8.471      1.000       0.500     72    27.3   264     ERRMC  
     BURIED  . . . . . . . .    6.137      1.000       0.500     54    50.5   107     ERRMC  
     CORE  . . . . . . . . .    7.078      1.000       0.500    102    47.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.948      1.000       0.500     22     7.7   284     ERRSC  
     WELL ORDERED  . . . . .    6.948      1.000       0.500     22     7.7   284     ERRSC  
     NO INTER CONTACTS . . .    6.948      1.000       0.500     22     7.7   284     ERRSC  
     RELIABLE SIDE CHAINS  .    6.948      1.000       0.500     22     9.2   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    6.484      1.000       0.500     19     7.3   262     ERRSC  
     ALTERNATIVE PARENT  . .    1.076      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    6.457      1.000       0.500     15    15.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    9.596      1.000       0.500      4     3.6   112     ERRSC  
     SURFACE . . . . . . . .    7.666      1.000       0.500     12     5.4   222     ERRSC  
     BURIED  . . . . . . . .    6.085      1.000       0.500     10    16.1    62     ERRSC  
     CORE  . . . . . . . . .    6.359      1.000       0.500     18    10.5   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.471      1.000       0.500    126    21.4   588     ERRALL 
     WELL ORDERED  . . . . .    7.471      1.000       0.500    126    21.4   588     ERRALL 
     NO INTER CONTACTS . . .    7.471      1.000       0.500    126    21.4   588     ERRALL 
     SHIFTED CHAIN . . . . .    7.098      1.000       0.500    111    20.5   542     ERRALL 
     ALTERNATIVE PARENT  . .    0.740      1.000       0.500      5    11.1    45     ERRALL 
     SECONDARY STRUCTURE . .    6.735      1.000       0.500     87    42.0   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    9.140      1.000       0.500     24    10.0   240     ERRALL 
     SURFACE . . . . . . . .    8.471      1.000       0.500     72    16.4   438     ERRALL 
     BURIED  . . . . . . . .    6.137      1.000       0.500     54    36.0   150     ERRALL 
     CORE  . . . . . . . . .    7.078      1.000       0.500    102    29.3   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         6         7        11        17      26      76   DISTCA 
CA  (P)      2.63      7.89      9.21     14.47     22.37              76   DISTCA 
CA  (RMS)    0.74      1.12      1.37      2.53      4.49                   DISTCA 
 
ALL (N)         7        24        34        56        83     126     588   DISTALL 
ALL (P)      1.19      4.08      5.78      9.52     14.12             588   DISTALL 
ALL (RMS)    0.75      1.24      1.75      2.80      4.71                   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            21             5          RMSLSI 
CA  (P)       57.89         27.63          6.58          RMSLSI 
CA  (RMS)      1.67          9.18         10.08          RMSLSI 
 
 
 
END of the results output 
