 
####################################################### 
#                                                     # 
#                        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 432 atoms, 390 common with TARGET 
           Number of atoms possible to evaluate: 330 
 
 
 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 . . . . . . . . . .    82.12           30.6   134    89.3   150     ARMSMC  
     WELL ORDERED  . . . . .    82.12           30.6   134    89.3   150     ARMSMC  
     NO INTER CONTACTS . . .    82.12           30.6   134    89.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    82.71           30.3   122    88.4   138     ARMSMC  
     ALTERNATIVE PARENT  . .    71.24           30.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    64.89           44.4    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    95.50           21.6    51    82.3    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    90.63           26.6    94    88.7   106     ARMSMC  
     BURIED  . . . . . . . .    57.33           40.0    40    90.9    44     ARMSMC  
     CORE  . . . . . . . . .    72.68           36.1    83    94.3    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) =  -0.21926     r(1,2) =  -0.36841     r(1,3) =   0.90344 
 r(2,1) =  -0.59322     r(2,2) =  -0.68481     r(2,3) =  -0.42323 
 r(3,1) =   0.77461     r(3,2) =  -0.62873     r(3,3) =  -0.06840 
THE OFFSET VECTOR: 
 v(1) =   5.71469     v(2) =  31.05819     v(3) =  26.08396 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.97           (Number of atoms:   11) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   17.05         69    90.8    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2471                            CRMSCA  
     WELL ORDERED  . . . . .   17.05         69    90.8    76     CRMSCA  
     NO INTER CONTACTS . . .   17.05         69    90.8    76     CRMSCA  
     SHIFTED CHAIN . . . . .   16.46         63    90.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .   14.65          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   18.18         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .   18.38          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   17.56         27    84.4    32     CRMSCA  
     SURFACE . . . . . . . .   17.82         49    90.7    54     CRMSCA  
     BURIED  . . . . . . . .   14.99         20    90.9    22     CRMSCA  
     CORE  . . . . . . . . .   16.71         42    95.5    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   17.08        330    88.9   371     CRMSMC  
     WELL ORDERED  . . . . .   17.08        330    88.9   371     CRMSMC  
     NO INTER CONTACTS . . .   17.08        330    88.9   371     CRMSMC  
     SHIFTED CHAIN . . . . .   16.48        300    88.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .   14.48         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   18.06        132    99.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .   18.19         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   17.76        125    81.2   154     CRMSMC  
     SURFACE . . . . . . . .   17.88        233    88.3   264     CRMSMC  
     BURIED  . . . . . . . .   14.99         97    90.7   107     CRMSMC  
     CORE  . . . . . . . . .   16.64        205    94.5   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   17.76         54    19.0   284     CRMSSC  
     WELL ORDERED  . . . . .   17.76         54    19.0   284     CRMSSC  
     NO INTER CONTACTS . . .   17.76         54    19.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   17.76         54    22.5   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   18.00         24    24.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   19.32         17    15.2   112     CRMSSC  
     SURFACE . . . . . . . .   19.05         37    16.7   222     CRMSSC  
     BURIED  . . . . . . . .   14.54         17    27.4    62     CRMSSC  
     CORE  . . . . . . . . .   16.99         37    21.5   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   17.08        330    56.1   588     CRMSALL 
     WELL ORDERED  . . . . .   17.08        330    56.1   588     CRMSALL 
     NO INTER CONTACTS . . .   17.08        330    56.1   588     CRMSALL 
     SHIFTED CHAIN . . . . .   16.48        300    55.4   542     CRMSALL 
     ALTERNATIVE PARENT  . .   14.48         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .   18.06        132    63.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   17.76        125    52.1   240     CRMSALL 
     SURFACE . . . . . . . .   17.88        233    53.2   438     CRMSALL 
     BURIED  . . . . . . . .   14.99         97    64.7   150     CRMSALL 
     CORE  . . . . . . . . .   16.64        205    58.9   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    25.75      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     1.99      3   100.0     3      26-GGG-28   
 CA  LOOP  3    18.03      5    50.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     9.74      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    25.75     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     2.55     12   100.0    12      26-GGG-28   
 MC  LOOP  3    18.40     23    46.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     9.76     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    25.75     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2     2.55     12   100.0    12      26-GGG-28   
 ALL LOOP  3    18.40     23    26.4    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     9.76     18    51.4    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.09      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.22      3   100.0     3      26-GGG-28   
 CA  LOOP  3     1.74      5    50.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.73      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.69     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.44     12   100.0    12      26-GGG-28   
 MC  LOOP  3     2.33     23    46.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.98     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.69     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2     1.44     12   100.0    12      26-GGG-28   
 ALL LOOP  3     2.33     23    26.4    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.98     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 . . . . . . . . . .   14.195      1.000       0.500     69    90.8    76     ERRCA  
     WELL ORDERED  . . . . .   14.195      1.000       0.500     69    90.8    76     ERRCA  
     NO INTER CONTACTS . . .   14.195      1.000       0.500     69    90.8    76     ERRCA  
     SHIFTED CHAIN . . . . .   13.614      1.000       0.500     63    90.0    70     ERRCA  
     ALTERNATIVE PARENT  . .   13.649      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .   15.791      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   15.006      1.000       0.500     27    84.4    32     ERRCA  
     SURFACE . . . . . . . .   14.926      1.000       0.500     49    90.7    54     ERRCA  
     BURIED  . . . . . . . .   12.403      1.000       0.500     20    90.9    22     ERRCA  
     CORE  . . . . . . . . .   13.673      1.000       0.500     42    95.5    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.285      1.000       0.500    330    88.9   371     ERRMC  
     WELL ORDERED  . . . . .   14.285      1.000       0.500    330    88.9   371     ERRMC  
     NO INTER CONTACTS . . .   14.285      1.000       0.500    330    88.9   371     ERRMC  
     SHIFTED CHAIN . . . . .   13.690      1.000       0.500    300    88.0   341     ERRMC  
     ALTERNATIVE PARENT  . .   13.612      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .   15.615      1.000       0.500    132    99.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   15.286      1.000       0.500    125    81.2   154     ERRMC  
     SURFACE . . . . . . . .   15.083      1.000       0.500    233    88.3   264     ERRMC  
     BURIED  . . . . . . . .   12.368      1.000       0.500     97    90.7   107     ERRMC  
     CORE  . . . . . . . . .   13.675      1.000       0.500    205    94.5   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   15.156      1.000       0.500     54    19.0   284     ERRSC  
     WELL ORDERED  . . . . .   15.156      1.000       0.500     54    19.0   284     ERRSC  
     NO INTER CONTACTS . . .   15.156      1.000       0.500     54    19.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .   15.156      1.000       0.500     54    22.5   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   14.504      1.000       0.500     48    18.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   14.493      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .   15.577      1.000       0.500     24    24.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   16.989      1.000       0.500     17    15.2   112     ERRSC  
     SURFACE . . . . . . . .   16.360      1.000       0.500     37    16.7   222     ERRSC  
     BURIED  . . . . . . . .   12.535      1.000       0.500     17    27.4    62     ERRSC  
     CORE  . . . . . . . . .   14.313      1.000       0.500     37    21.5   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.285      1.000       0.500    330    56.1   588     ERRALL 
     WELL ORDERED  . . . . .   14.285      1.000       0.500    330    56.1   588     ERRALL 
     NO INTER CONTACTS . . .   14.285      1.000       0.500    330    56.1   588     ERRALL 
     SHIFTED CHAIN . . . . .   13.690      1.000       0.500    300    55.4   542     ERRALL 
     ALTERNATIVE PARENT  . .   13.612      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .   15.615      1.000       0.500    132    63.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   15.286      1.000       0.500    125    52.1   240     ERRALL 
     SURFACE . . . . . . . .   15.083      1.000       0.500    233    53.2   438     ERRALL 
     BURIED  . . . . . . . .   12.368      1.000       0.500     97    64.7   150     ERRALL 
     CORE  . . . . . . . . .   13.675      1.000       0.500    205    58.9   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        11        16        25      69      76   DISTCA 
CA  (P)      1.32      6.58     14.47     21.05     32.89              76   DISTCA 
CA  (RMS)    0.96      1.48      1.97      2.73      4.81                   DISTCA 
 
ALL (N)         4        20        43        81       123     330     588   DISTALL 
ALL (P)      0.68      3.40      7.31     13.78     20.92             588   DISTALL 
ALL (RMS)    0.82      1.44      2.05      2.99      5.22                   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            42            27          RMSLSI 
CA  (P)       57.89         55.26         35.53          RMSLSI 
CA  (RMS)      1.67         16.71         17.56          RMSLSI 
 
 
 
END of the results output 
