 
####################################################### 
#                                                     # 
#                        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      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_2.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_2.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_2.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_2.1aj4.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 1062 atoms, MODEL 621 atoms, 69 common with TARGET 
           Number of atoms possible to evaluate: 69 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 3.538625 
 
 CA-RMS TARGET<->PARENT(1ncx)	 3.287245 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.396291 
 
 CA-RMS TARGET<->PARENT(1aj4)	 5.635736 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   136     ARMSMC  
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   136     ARMSMC  
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   136     ARMSMC  
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0   136     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSMC  
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   116     ARMSMC  
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    20     ARMSMC  
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    40     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    52     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    31     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    43     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     4     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.50649     r(1,2) =  -0.78489     r(1,3) =  -0.35696 
 r(2,1) =  -0.28053     r(2,2) =  -0.54147     r(2,3) =   0.79254 
 r(3,1) =  -0.81534     r(3,2) =  -0.30127     r(3,3) =  -0.49443 
THE OFFSET VECTOR: 
 v(1) = -81.69370     v(2) = -39.63601     v(3) =  66.68192 
 
 Number of iteration 54                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.71           (Number of atoms:   28) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.86         69   100.0    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0849                            CRMSCA  
     WELL ORDERED  . . . . .    5.86         69   100.0    69     CRMSCA  
     NO INTER CONTACTS . . .    5.86         69   100.0    69     CRMSCA  
     SHIFTED CHAIN . . . . .    5.86         69   100.0    69     CRMSCA  
     ALTERNATIVE PARENT  . .    9.23          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .    5.96         36   100.0    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.00         58   100.0    58     CRMSCA  
     SURFACE . . . . . . . .    6.13         59   100.0    59     CRMSCA  
     BURIED  . . . . . . . .    3.86         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .    5.07         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.86         69    20.5   337     CRMSMC  
     WELL ORDERED  . . . . .    5.86         69    20.5   337     CRMSMC  
     NO INTER CONTACTS . . .    5.86         69    20.5   337     CRMSMC  
     SHIFTED CHAIN . . . . .    5.86         69    20.5   337     CRMSMC  
     ALTERNATIVE PARENT  . .    9.23          1    20.0     5     CRMSMC  
     SECONDARY STRUCTURE . .    5.96         36    20.5   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.00         58    20.5   283     CRMSMC  
     SURFACE . . . . . . . .    6.13         59    20.3   290     CRMSMC  
     BURIED  . . . . . . . .    3.86         10    21.3    47     CRMSMC  
     CORE  . . . . . . . . .    5.07         11    20.4    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   786     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   786     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   786     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   742     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   158     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   666     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   689     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    97     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.86         69     6.5  1062     CRMSALL 
     WELL ORDERED  . . . . .    5.86         69     6.5  1062     CRMSALL 
     NO INTER CONTACTS . . .    5.86         69     6.5  1062     CRMSALL 
     SHIFTED CHAIN . . . . .    5.86         69     6.5  1062     CRMSALL 
     ALTERNATIVE PARENT  . .    9.23          1     7.1    14     CRMSALL 
     SECONDARY STRUCTURE . .    5.96         36     6.3   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.00         58     6.5   898     CRMSALL 
     SURFACE . . . . . . . .    6.13         59     6.4   925     CRMSALL 
     BURIED  . . . . . . . .    3.86         10     7.3   137     CRMSALL 
     CORE  . . . . . . . . .    5.07         11     6.7   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    12.56      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     3.09     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     3.62     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    12.56      9    20.5    44      72-PGDPEEFVK-80   
 MC  LOOP  2     3.09     23    20.7   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     3.62     24    20.3   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    12.56      9     6.7   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.09     23     6.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     3.62     24     6.2   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.20      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.91     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     3.16     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.20      9    20.5    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.91     23    20.7   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     3.16     24    20.3   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.20      9     6.7   135      72-PGDPEEFVK-80   
 ALL LOOP  2     2.91     23     6.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     3.16     24     6.2   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.509      1.000       0.500     69   100.0    69     ERRCA  
     WELL ORDERED  . . . . .    4.509      1.000       0.500     69   100.0    69     ERRCA  
     NO INTER CONTACTS . . .    4.509      1.000       0.500     69   100.0    69     ERRCA  
     SHIFTED CHAIN . . . . .    4.509      1.000       0.500     69   100.0    69     ERRCA  
     ALTERNATIVE PARENT  . .    9.228      1.000       0.500      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    4.246      1.000       0.500     36   100.0    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.533      1.000       0.500     58   100.0    58     ERRCA  
     SURFACE . . . . . . . .    4.760      1.000       0.500     59   100.0    59     ERRCA  
     BURIED  . . . . . . . .    3.027      1.000       0.500     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    4.380      1.000       0.500     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.509      1.000       0.500     69    20.5   337     ERRMC  
     WELL ORDERED  . . . . .    4.509      1.000       0.500     69    20.5   337     ERRMC  
     NO INTER CONTACTS . . .    4.509      1.000       0.500     69    20.5   337     ERRMC  
     SHIFTED CHAIN . . . . .    4.509      1.000       0.500     69    20.5   337     ERRMC  
     ALTERNATIVE PARENT  . .    9.228      1.000       0.500      1    20.0     5     ERRMC  
     SECONDARY STRUCTURE . .    4.246      1.000       0.500     36    20.5   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.533      1.000       0.500     58    20.5   283     ERRMC  
     SURFACE . . . . . . . .    4.760      1.000       0.500     59    20.3   290     ERRMC  
     BURIED  . . . . . . . .    3.027      1.000       0.500     10    21.3    47     ERRMC  
     CORE  . . . . . . . . .    4.380      1.000       0.500     11    20.4    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   742     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   158     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    10     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   429     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   666     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   689     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    97     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.509      1.000       0.500     69     6.5  1062     ERRALL 
     WELL ORDERED  . . . . .    4.509      1.000       0.500     69     6.5  1062     ERRALL 
     NO INTER CONTACTS . . .    4.509      1.000       0.500     69     6.5  1062     ERRALL 
     SHIFTED CHAIN . . . . .    4.509      1.000       0.500     69     6.5  1062     ERRALL 
     ALTERNATIVE PARENT  . .    9.228      1.000       0.500      1     7.1    14     ERRALL 
     SECONDARY STRUCTURE . .    4.246      1.000       0.500     36     6.3   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.533      1.000       0.500     58     6.5   898     ERRALL 
     SURFACE . . . . . . . .    4.760      1.000       0.500     59     6.4   925     ERRALL 
     BURIED  . . . . . . . .    3.027      1.000       0.500     10     7.3   137     ERRALL 
     CORE  . . . . . . . . .    4.380      1.000       0.500     11     6.7   164     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)         4        19        31        47        62      69      69   DISTCA 
CA  (P)      5.80     27.54     44.93     68.12     89.86              69   DISTCA 
CA  (RMS)    0.54      1.40      1.85      2.57      4.24                   DISTCA 
 
ALL (N)         4        19        31        47        62      69    1062   DISTALL 
ALL (P)      0.38      1.79      2.92      4.43      5.84            1062   DISTALL 
ALL (RMS)    0.54      1.40      1.85      2.57      4.24                   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)          11            11            58          RMSLSI 
CA  (P)       15.94         15.94         84.06          RMSLSI 
CA  (RMS)      1.81          5.07          6.00          RMSLSI 
 
 
 
END of the results output 
