 
####################################################### 
#                                                     # 
#                        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 415 atoms, 377 common with TARGET 
           Number of atoms possible to evaluate: 351 
 
 
 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 . . . . . . . . . .    82.90           34.8   138    92.0   150     ARMSMC  
     WELL ORDERED  . . . . .    82.90           34.8   138    92.0   150     ARMSMC  
     NO INTER CONTACTS . . .    82.90           34.8   138    92.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    83.21           34.4   128    92.8   138     ARMSMC  
     ALTERNATIVE PARENT  . .    72.50           22.2     9    90.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    68.69           44.2    43    79.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    86.74           37.1    62   100.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    87.82           34.3    99    93.4   106     ARMSMC  
     BURIED  . . . . . . . .    68.87           35.9    39    88.6    44     ARMSMC  
     CORE  . . . . . . . . .    79.64           32.9    76    86.4    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) =  -0.21652     r(1,2) =  -0.18184     r(1,3) =  -0.95919 
 r(2,1) =  -0.57920     r(2,2) =  -0.76699     r(2,3) =   0.27614 
 r(3,1) =  -0.78590     r(3,2) =   0.61536     r(3,3) =   0.06075 
THE OFFSET VECTOR: 
 v(1) =   4.67510     v(2) =  35.59743     v(3) =   7.68562 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.42           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   13.91         73    96.1    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1906                            CRMSCA  
     WELL ORDERED  . . . . .   13.91         73    96.1    76     CRMSCA  
     NO INTER CONTACTS . . .   13.91         73    96.1    76     CRMSCA  
     SHIFTED CHAIN . . . . .   13.49         68    97.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .   12.06          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   16.42         24    88.9    27     CRMSCA  
     SHIFTED SS UNITS  . . .   12.75          5    83.3     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.49         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .   13.94         52    96.3    54     CRMSCA  
     BURIED  . . . . . . . .   13.84         21    95.5    22     CRMSCA  
     CORE  . . . . . . . . .   15.54         41    93.2    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.88        351    94.6   371     CRMSMC  
     WELL ORDERED  . . . . .   13.88        351    94.6   371     CRMSMC  
     NO INTER CONTACTS . . .   13.88        351    94.6   371     CRMSMC  
     SHIFTED CHAIN . . . . .   13.40        326    95.6   341     CRMSMC  
     ALTERNATIVE PARENT  . .   12.08         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   16.14        117    88.0   133     CRMSMC  
     SHIFTED SS UNITS  . . .   12.89         25    83.3    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.54        152    98.7   154     CRMSMC  
     SURFACE . . . . . . . .   14.03        250    94.7   264     CRMSMC  
     BURIED  . . . . . . . .   13.52        101    94.4   107     CRMSMC  
     CORE  . . . . . . . . .   15.44        199    91.7   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   14.39         59    20.8   284     CRMSSC  
     WELL ORDERED  . . . . .   14.39         59    20.8   284     CRMSSC  
     NO INTER CONTACTS . . .   14.39         59    20.8   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.39         59    24.6   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   15.75         21    21.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   11.45         24    21.4   112     CRMSSC  
     SURFACE . . . . . . . .   15.29         42    18.9   222     CRMSSC  
     BURIED  . . . . . . . .   11.85         17    27.4    62     CRMSSC  
     CORE  . . . . . . . . .   16.09         35    20.3   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.88        351    59.7   588     CRMSALL 
     WELL ORDERED  . . . . .   13.88        351    59.7   588     CRMSALL 
     NO INTER CONTACTS . . .   13.88        351    59.7   588     CRMSALL 
     SHIFTED CHAIN . . . . .   13.40        326    60.1   542     CRMSALL 
     ALTERNATIVE PARENT  . .   12.08         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .   16.14        117    56.5   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   11.54        152    63.3   240     CRMSALL 
     SURFACE . . . . . . . .   14.03        250    57.1   438     CRMSALL 
     BURIED  . . . . . . . .   13.52        101    67.3   150     CRMSALL 
     CORE  . . . . . . . . .   15.44        199    57.2   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    13.91      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     4.96      3   100.0     3      26-GGG-28   
 CA  LOOP  3     6.53     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    15.36      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    13.74     33    97.1    34       1-AEIEVGR-7    
 MC  LOOP  2     5.25     12   100.0    12      26-GGG-28   
 MC  LOOP  3     6.60     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    15.39     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    13.74     33    62.3    53       1-AEIEVGR-7    
 ALL LOOP  2     5.25     12   100.0    12      26-GGG-28   
 ALL LOOP  3     6.60     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    15.39     18    51.4    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.34      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.04      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.53     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     2.34      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.60     33    97.1    34       1-AEIEVGR-7    
 MC  LOOP  2     1.51     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.68     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.45     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.60     33    62.3    53       1-AEIEVGR-7    
 ALL LOOP  2     1.51     12   100.0    12      26-GGG-28   
 ALL LOOP  3     3.68     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.45     18    51.4    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 . . . . . . . . . .   12.008      1.000       0.500     73    96.1    76     ERRCA  
     WELL ORDERED  . . . . .   12.008      1.000       0.500     73    96.1    76     ERRCA  
     NO INTER CONTACTS . . .   12.008      1.000       0.500     73    96.1    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.623      1.000       0.500     68    97.1    70     ERRCA  
     ALTERNATIVE PARENT  . .   11.699      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .   14.653      1.000       0.500     24    88.9    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   10.330      1.000       0.500     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .   11.974      1.000       0.500     52    96.3    54     ERRCA  
     BURIED  . . . . . . . .   12.091      1.000       0.500     21    95.5    22     ERRCA  
     CORE  . . . . . . . . .   13.317      1.000       0.500     41    93.2    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.070      1.000       0.500    351    94.6   371     ERRMC  
     WELL ORDERED  . . . . .   12.070      1.000       0.500    351    94.6   371     ERRMC  
     NO INTER CONTACTS . . .   12.070      1.000       0.500    351    94.6   371     ERRMC  
     SHIFTED CHAIN . . . . .   11.644      1.000       0.500    326    95.6   341     ERRMC  
     ALTERNATIVE PARENT  . .   11.700      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .   14.407      1.000       0.500    117    88.0   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.419      1.000       0.500    152    98.7   154     ERRMC  
     SURFACE . . . . . . . .   12.134      1.000       0.500    250    94.7   264     ERRMC  
     BURIED  . . . . . . . .   11.912      1.000       0.500    101    94.4   107     ERRMC  
     CORE  . . . . . . . . .   13.331      1.000       0.500    199    91.7   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.728      1.000       0.500     59    20.8   284     ERRSC  
     WELL ORDERED  . . . . .   12.728      1.000       0.500     59    20.8   284     ERRSC  
     NO INTER CONTACTS . . .   12.728      1.000       0.500     59    20.8   284     ERRSC  
     RELIABLE SIDE CHAINS  .   12.728      1.000       0.500     59    24.6   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   12.303      1.000       0.500     54    20.6   262     ERRSC  
     ALTERNATIVE PARENT  . .   11.859      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .   14.221      1.000       0.500     21    21.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.377      1.000       0.500     24    21.4   112     ERRSC  
     SURFACE . . . . . . . .   13.508      1.000       0.500     42    18.9   222     ERRSC  
     BURIED  . . . . . . . .   10.798      1.000       0.500     17    27.4    62     ERRSC  
     CORE  . . . . . . . . .   14.339      1.000       0.500     35    20.3   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.070      1.000       0.500    351    59.7   588     ERRALL 
     WELL ORDERED  . . . . .   12.070      1.000       0.500    351    59.7   588     ERRALL 
     NO INTER CONTACTS . . .   12.070      1.000       0.500    351    59.7   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.644      1.000       0.500    326    60.1   542     ERRALL 
     ALTERNATIVE PARENT  . .   11.700      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .   14.407      1.000       0.500    117    56.5   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.419      1.000       0.500    152    63.3   240     ERRALL 
     SURFACE . . . . . . . .   12.134      1.000       0.500    250    57.1   438     ERRALL 
     BURIED  . . . . . . . .   11.912      1.000       0.500    101    67.3   150     ERRALL 
     CORE  . . . . . . . . .   13.331      1.000       0.500    199    57.2   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)         3         5         6        10        32      73      76   DISTCA 
CA  (P)      3.95      6.58      7.89     13.16     42.11              76   DISTCA 
CA  (RMS)    0.78      1.13      1.42      3.04      6.43                   DISTCA 
 
ALL (N)         6        15        25        51       151     351     588   DISTALL 
ALL (P)      1.02      2.55      4.25      8.67     25.68             588   DISTALL 
ALL (RMS)    0.71      1.23      1.92      3.28      6.51                   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            41            32          RMSLSI 
CA  (P)       57.89         53.95         42.11          RMSLSI 
CA  (RMS)      1.67         15.54         11.49          RMSLSI 
 
 
 
END of the results output 
