#CCP4I VERSION CCP4Interface 1.4.4 #CCP4I SCRIPT LOG refmac5 #CCP4I DATE 17 Jul 2007 11:42:19 #CCP4I USER pjx #CCP4I PROJECT PROJECT #CCP4I JOB_ID 156 #CCP4I SCRATCH /tmp/pjx #CCP4I HOSTNAME ccp4t.dl.ac.uk #CCP4I PID 10399 
 
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 ### CCP4 6.0: Refmac_5.3.0040    version 5.3.0040  : 12/07/07##
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 User: pjx  Run date: 17/ 7/2007 Run time: 11:42:19 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Data line--- make check NONE
 MAKE
 Data line--- make     hydrogen YES     hout NO     peptide NO     cispeptide YES     ssbridge YES     symmetry YES     sugar YES     connectivity NO     link NO
 MAKE
 Data line--- refi     type REST     resi MLKF     meth CGMAT     bref ISOT
 REFI
 Data line--- ncyc 5
 NCYC
 Data line--- scal     type SIMP     reso 1.833 50.000     LSSC     ANISO     EXPE
 SCAL
 Data line--- solvent YES     VDWProb 1.2     IONProb 0.8     RSHRink 0.8
 SOLV
 Data line--- weight     AUTO
 WEIG
 Data line--- monitor MEDIUM     torsion 10.0     distance 10.0     angle 10.0     plane 10.0     chiral 10.0     bfactor 10.0     bsphere 10.0     rbond 10.0     ncsr 10.0
 MONI
 Data line--- labin  FP=FNAT SIGFP=SIGFNAT    FREE=FreeR_flag
 LABI
 Data line--- labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
 LABO
 Data line--- PNAME RNASE
 PNAM
 Data line--- DNAME NATIVE
 DNAM
 Data line--- RSIZE 80
 RSIZ
 Data line--- END
 END 

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase18.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/syminfo.lib

 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - /home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /tmp/pjx/PROJECT_156_2_pdb_1.tmp
Input reflection file.  Logical name - HKLIN actual file name  - /home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase18.mtz
Output reflection file. Logical name - HKLOUT actual file name - /tmp/pjx/PROJECT_156_3_mtz_1.tmp
 
Cell from mtz :    64.897    78.323    38.792    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens in input coordinate file will be kept
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Rice Maximum Likelihood for Fs
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0149
  Refinement of individual isotropic Bfactors
  Refinement resln        :    50.0000  1.8330
  Estimated number of reflections :      23839
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :     5
  Scaling type                           :
          Wilson using 1 Gaussian
  using working set of reflns and experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas
 
  Scaling and SigmaA resln:    50.0000  1.8330
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00
 
 RADIUS OF CONFIDENCE
     Positional parameters 0.30A
     Thermal parameters    0.03A**2
     Occupancy parameters  0.50
 
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------
 
 Input file :/home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.30
 _lib_update       02/03/07
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2433
                with complete description    :   450
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    64
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/atomsf.lib


  Number of atoms    :    1725
  Number of residues :     417
  Number of chains   :       5
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =      3.78
            ch:AA   res:  26  GLY      -->  27  PRO
  WARNING : CIS peptide bond is found, angle =      0.13
            ch:BB   res:  26  GLY      -->  27  PRO
  WARNING : link:SS       is found dist =     1.959 ideal_dist=     2.031
            ch:AA   res:   7  CYS      at:SG  .->AA   res:  96  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.042 ideal_dist=     2.031
            ch:BB   res:   7  CYS      at:SG  .->BB   res:  96  CYS      at:SG  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  Number of chains                  :       5
  Total number of monomers          :     417
  Number of atoms                   :    1725
  Number of missing atoms           :       0
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :    1538
  Number of angles restraints   :    2108
  Number of torsions restraints :    1036
  Number of chiralities         :     234
  Number of planar groups       :     278
 
 
 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c
 
 
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
 
 
 Number of reflections in file      17991
 Number of reflection read          17980
 
 
     CGMAT cycle number =      1
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
B     75 ALA C   . - B     76 THR N   . mod.= 1.564 id.= 1.329 dev= -0.235 sig.= 0.014
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A     40 ARG CD    - A     40 ARG CZ    mod.= 163.02 id.= 124.20 dev=-38.819 sig.=  1.500
A     54 GLU CA    - A     54 GLU CG    mod.= 146.91 id.= 114.10 dev=-32.813 sig.=  2.000
B      3 SER CA    - B      3 SER OG    mod.=  89.21 id.= 111.10 dev= 21.890 sig.=  2.000
B     40 ARG CA    - B     40 ARG CG    mod.= 151.13 id.= 114.10 dev=-37.029 sig.=  2.000
B     40 ARG CD    - B     40 ARG CZ    mod.= 156.99 id.= 124.20 dev=-32.795 sig.=  1.500
 
    ****                  B-value outliers                  ****
 
B-value differences >  10.00Sigma will be monitored
A      1 ASP CG    - A      1 ASP CA       ABS(DELTA)= 20.840   Sigma=  2.000
A     25 ASP CG    - A     25 ASP CA       ABS(DELTA)= 24.000   Sigma=  2.000
B      5 THR CB    - B      5 THR CA       ABS(DELTA)= 15.830   Sigma=  1.500
 
 weigth matrix   0.8005419    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1538     0.028     0.022
Bond angles  : refined atoms                   2108     4.533     1.964
Torsion angles, period  1. refined              190     3.891     5.000
Torsion angles, period  2. refined               74    31.700    23.784
Torsion angles, period  3. refined              216    14.007    15.000
Torsion angles, period  4. refined               10    21.347    15.000
Chiral centres: refined atoms                   234     0.163     0.200
Planar groups: refined atoms                   1212     0.016     0.020
VDW repulsions: refined atoms                   624     0.239     0.200
VDW; torsion: refined atoms                    1067     0.317     0.200
HBOND: refined atoms                            121     0.179     0.200
VDW repulsions; symmetry: refined atoms          47     0.212     0.200
HBOND; symmetry: refined atoms                   27     0.394     0.200
M. chain bond B values: refined atoms           956     3.209     1.500
M. chain angle B values: refined atoms         1558     4.517     2.000
S. chain bond B values: refined atoms           582     4.562     3.000
S. chain angle B values: refined atoms          550     6.301     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.845, B  =   1.075
Partial structure    1: scale =    0.299, B  =  27.184
Overall anisotropic scale factors
   B11 = -0.57 B22 =  0.42 B33 =  0.15 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008     243 100.00   359.9   361.6  0.21  0.25      10   336.0   324.8  0.13  0.17
 0.023     384 100.00   281.6   287.1  0.20  0.25      21   274.3   296.7  0.24  0.31
 0.038     477 100.00   314.7   310.3  0.17  0.21      28   308.0   317.3  0.14  0.20
 0.052     544  96.62   346.7   340.7  0.16  0.21      27   408.9   408.4  0.13  0.15
 0.067     612  98.32   317.3   309.0  0.18  0.23      33   304.9   271.8  0.21  0.26
 0.082     676  99.58   302.8   286.0  0.18  0.22      41   289.4   251.3  0.20  0.22
 0.097     737  99.87   256.5   243.3  0.21  0.23      38   277.5   262.6  0.17  0.20
 0.112     771  99.64   210.7   201.5  0.21  0.23      53   214.1   199.0  0.24  0.25
 0.127     831  99.77   181.9   173.2  0.24  0.25      44   208.8   184.7  0.24  0.27
 0.142     868  99.78   164.7   158.2  0.25  0.25      47   149.3   148.1  0.26  0.25
 0.156     940  99.60   153.8   147.9  0.25  0.26      51   136.2   131.6  0.25  0.23
 0.171     934  99.20   134.6   129.4  0.25  0.24      60   128.3   125.0  0.23  0.23
 0.186     995  99.15   127.1   121.9  0.26  0.25      55   123.8   120.3  0.22  0.23
 0.201    1029  99.00   119.8   113.5  0.25  0.24      58   122.1   122.5  0.23  0.22
 0.216    1043  98.30   114.7   106.6  0.27  0.25      55    96.0    97.6  0.32  0.30
 0.231    1083  97.76   101.5    97.7  0.27  0.25      53   100.2    93.2  0.26  0.25
 0.246    1132  97.54    96.7    92.3  0.27  0.25      59   103.1   103.0  0.24  0.23
 0.260    1128  96.73    85.9    84.5  0.28  0.26      54    84.0    84.5  0.24  0.21
 0.275    1144  93.70    73.7    75.8  0.30  0.26      61    72.1    72.0  0.33  0.28
 0.290     758  61.35    59.1    70.9  0.43  0.35      34    54.1    66.7  0.49  0.38
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    1. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0078   131   0.917   112   0.808   243   0.867  1.021
  0.0227   270   0.869   114   0.776   384   0.842  1.014
  0.0375   359   0.898   118   0.824   477   0.880  1.008
  0.0524   438   0.935   106   0.828   544   0.914  1.001
  0.0673   500   0.931   112   0.850   612   0.916  0.994
  0.0821   565   0.931   111   0.852   676   0.918  0.988
  0.0970   623   0.905   114   0.836   737   0.894  0.981
  0.1118   657   0.895   114   0.812   771   0.883  0.975
  0.1267   717   0.881   114   0.789   831   0.868  0.968
  0.1416   759   0.856   109   0.812   868   0.850  0.962
  0.1564   823   0.864   117   0.812   940   0.857  0.955
  0.1713   825   0.854   109   0.766   934   0.843  0.949
  0.1861   882   0.854   113   0.750   995   0.842  0.943
  0.2010   919   0.853   110   0.787  1029   0.846  0.936
  0.2158   936   0.846   107   0.814  1043   0.843  0.930
  0.2307   982   0.841   101   0.751  1083   0.832  0.924
  0.2456  1021   0.843   111   0.778  1132   0.837  0.918
  0.2604  1032   0.828    96   0.743  1128   0.821  0.912
  0.2753  1046   0.809    98   0.731  1144   0.803  0.906
  0.2901   719   0.777    39   0.816   758   0.779  0.900
 $$
Resolution limits                    =     50.000     1.833
Number of used reflections           =      16329
Percentage observed                  =    95.7230
Percentage of free reflections       =     5.1246
Overall R factor                     =     0.2283
Free R factor                        =     0.2206
Overall weighted R factor            =     0.2396
Free weighted R factor               =     0.2345
Overall correlation coefficient      =     0.9305
Free correlation coefficient         =     0.9326
Cruickshanks DPI for coordinate error=     0.1848
DPI based on free R factor           =     0.1358
Overall figure of merit              =     0.8510
ML based su of positional parameters =     0.0941
ML based su of thermal parameters    =     3.1376
-----------------------------------------------------------------------------
 Trying gamma equal    0.000000    
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      2
 
 weigth matrix    1.099140    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1538     0.029     0.022
Bond angles  : refined atoms                   2108     2.509     1.964
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.847, B  =  -0.159
Partial structure    1: scale =    0.299, B  =  24.114
Overall anisotropic scale factors
   B11 = -0.57 B22 =  0.42 B33 =  0.15 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1843
Free R factor                        =     0.2013
Overall figure of merit              =     0.8721
-----------------------------------------------------------------------------
 Trying gamma equal    0.000000    
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      3
 
 weigth matrix    1.204761    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1538     0.030     0.022
Bond angles  : refined atoms                   2108     2.448     1.964
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.850, B  =  -0.013
Partial structure    1: scale =    0.300, B  =  21.474
Overall anisotropic scale factors
   B11 = -0.57 B22 =  0.42 B33 =  0.15 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1689
Free R factor                        =     0.1951
Overall figure of merit              =     0.8775
-----------------------------------------------------------------------------
 Trying gamma equal    0.000000    
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      4
 
 weigth matrix    1.239633    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1538     0.031     0.022
Bond angles  : refined atoms                   2108     2.431     1.964
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.851, B  =   0.003
Partial structure    1: scale =    0.300, B  =  20.537
Overall anisotropic scale factors
   B11 = -0.57 B22 =  0.42 B33 =  0.15 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1616
Free R factor                        =     0.1929
Overall figure of merit              =     0.8790
-----------------------------------------------------------------------------
 Trying gamma equal    0.000000    
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      5
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A     54 GLU CA    - A     54 GLU CG    mod.= 137.78 id.= 114.10 dev=-23.675 sig.=  2.000
 
 weigth matrix    1.248353    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1538     0.031     0.022
Bond angles  : refined atoms                   2108     2.404     1.964
Torsion angles, period  1. refined              190     6.167     5.000
Torsion angles, period  2. refined               74    29.023    23.784
Torsion angles, period  3. refined              216    13.599    15.000
Torsion angles, period  4. refined               10    17.672    15.000
Chiral centres: refined atoms                   234     0.202     0.200
Planar groups: refined atoms                   1212     0.013     0.020
VDW repulsions: refined atoms                   625     0.221     0.200
VDW; torsion: refined atoms                    1078     0.315     0.200
HBOND: refined atoms                            135     0.153     0.200
VDW repulsions; symmetry: refined atoms          49     0.154     0.200
HBOND; symmetry: refined atoms                   27     0.345     0.200
M. chain bond B values: refined atoms           970     1.781     1.500
M. chain angle B values: refined atoms         1558     2.722     2.000
S. chain bond B values: refined atoms           629     4.183     3.000
S. chain angle B values: refined atoms          550     6.406     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.852, B  =  -0.002
Partial structure    1: scale =    0.300, B  =  20.334
Overall anisotropic scale factors
   B11 = -0.57 B22 =  0.42 B33 =  0.15 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    5. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    5.  v. resln :N:1,6,7,11,12:
:Cycle    5.  and  v. resln :N:1,4,5,9,10:
:Cycle    5. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008     243 100.00   357.1   359.0  0.19  0.23      10   333.4   322.2  0.19  0.23
 0.023     384 100.00   279.4   292.0  0.17  0.21      21   272.1   300.3  0.20  0.28
 0.038     477 100.00   312.2   313.3  0.13  0.17      28   305.6   323.8  0.14  0.20
 0.052     544  96.62   344.0   338.7  0.12  0.15      27   405.7   398.3  0.11  0.14
 0.067     612  98.32   314.9   305.7  0.13  0.16      33   302.5   278.8  0.14  0.18
 0.082     676  99.58   300.4   285.2  0.14  0.16      41   287.1   260.8  0.19  0.23
 0.097     737  99.87   254.6   241.7  0.15  0.16      38   275.3   253.6  0.17  0.20
 0.112     771  99.64   209.0   201.4  0.15  0.16      53   212.4   195.8  0.20  0.21
 0.127     831  99.77   180.5   175.4  0.17  0.18      44   207.2   190.5  0.18  0.21
 0.142     868  99.78   163.5   159.8  0.17  0.18      47   148.1   150.2  0.22  0.23
 0.156     940  99.60   152.6   148.9  0.17  0.17      51   135.1   136.3  0.17  0.18
 0.171     934  99.20   133.6   131.3  0.17  0.17      60   127.3   123.4  0.24  0.24
 0.186     995  99.15   126.1   124.0  0.17  0.16      55   122.9   123.8  0.22  0.22
 0.201    1029  99.00   118.9   115.5  0.16  0.15      58   121.2   116.3  0.22  0.21
 0.216    1043  98.30   113.8   110.2  0.16  0.15      55    95.3    97.9  0.23  0.22
 0.231    1083  97.76   100.7   100.0  0.17  0.16      53    99.4    92.4  0.21  0.20
 0.246    1132  97.54    96.0    94.7  0.16  0.15      59   102.3   105.9  0.23  0.22
 0.260    1128  96.73    85.3    86.7  0.18  0.16      54    83.3    86.0  0.20  0.18
 0.275    1144  93.70    73.2    75.8  0.18  0.16      61    71.6    78.1  0.25  0.22
 0.290     758  61.35    58.7    69.4  0.30  0.24      34    53.7    71.4  0.43  0.29
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    5. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    5. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0078   131   0.937   112   0.832   243   0.889  1.020
  0.0227   270   0.901   114   0.811   384   0.874  1.015
  0.0375   359   0.915   118   0.855   477   0.900  1.010
  0.0524   438   0.946   106   0.894   544   0.936  1.004
  0.0673   500   0.946   112   0.850   612   0.928  0.999
  0.0821   565   0.942   111   0.866   676   0.929  0.994
  0.0970   623   0.926   114   0.870   737   0.917  0.989
  0.1118   657   0.916   114   0.838   771   0.905  0.984
  0.1267   717   0.900   114   0.836   831   0.891  0.979
  0.1416   759   0.886   109   0.827   868   0.879  0.974
  0.1564   823   0.888   117   0.831   940   0.881  0.969
  0.1713   825   0.880   109   0.803   934   0.871  0.964
  0.1861   882   0.882   113   0.787   995   0.871  0.959
  0.2010   919   0.878   110   0.859  1029   0.876  0.954
  0.2158   936   0.880   107   0.811  1043   0.873  0.949
  0.2307   982   0.870   101   0.780  1083   0.861  0.944
  0.2456  1021   0.878   111   0.816  1132   0.872  0.939
  0.2604  1032   0.863    96   0.813  1128   0.859  0.935
  0.2753  1046   0.844    98   0.773  1144   0.838  0.930
  0.2901   719   0.824    39   0.847   758   0.826  0.926
 $$
Resolution limits                    =     50.000     1.833
Number of used reflections           =      16329
Percentage observed                  =    95.7230
Percentage of free reflections       =     5.1246
Overall R factor                     =     0.1579
Free R factor                        =     0.1915
Overall weighted R factor            =     0.1682
Free weighted R factor               =     0.2089
Overall correlation coefficient      =     0.9643
Free correlation coefficient         =     0.9497
Cruickshanks DPI for coordinate error=     0.1278
DPI based on free R factor           =     0.1178
Overall figure of merit              =     0.8792
ML based su of positional parameters =     0.0754
ML based su of thermal parameters    =     2.4975
-----------------------------------------------------------------------------
 Trying gamma equal    0.000000    
 Convergence reached with no gamma cycles 

 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A     54 GLU CA    - A     54 GLU CG    mod.= 137.04 id.= 114.10 dev=-22.943 sig.=  2.000
 

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /tmp/pjx/PROJECT_156_3_mtz_1.tmp 

 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1538     0.031     0.022
Bond angles  : refined atoms                   2108     2.378     1.964
Torsion angles, period  1. refined              190     6.194     5.000
Torsion angles, period  2. refined               74    28.982    23.784
Torsion angles, period  3. refined              216    13.563    15.000
Torsion angles, period  4. refined               10    16.921    15.000
Chiral centres: refined atoms                   234     0.202     0.200
Planar groups: refined atoms                   1212     0.013     0.020
VDW repulsions: refined atoms                   627     0.220     0.200
VDW; torsion: refined atoms                    1082     0.315     0.200
HBOND: refined atoms                            134     0.150     0.200
VDW repulsions; symmetry: refined atoms          49     0.156     0.200
HBOND; symmetry: refined atoms                   28     0.330     0.200
M. chain bond B values: refined atoms           969     1.760     1.500
M. chain angle B values: refined atoms         1558     2.701     2.000
S. chain bond B values: refined atoms           635     4.150     3.000
S. chain angle B values: refined atoms          550     6.413     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.852, B  =   0.011
Partial structure    1: scale =    0.300, B  =  19.949
Overall anisotropic scale factors
   B11 = -0.57 B22 =  0.42 B33 =  0.15 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    6. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    6.  v. resln :N:1,6,7,11,12:
:Cycle    6.  and  v. resln :N:1,4,5,9,10:
:Cycle    6. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008     243 100.00   356.8   358.2  0.19  0.23      10   333.2   322.8  0.19  0.23
 0.023     384 100.00   279.2   292.0  0.17  0.21      21   271.9   301.3  0.20  0.27
 0.038     477 100.00   312.0   313.6  0.13  0.17      28   305.4   323.2  0.14  0.20
 0.052     544  96.62   343.8   338.9  0.11  0.15      27   405.4   397.6  0.10  0.13
 0.067     612  98.32   314.7   305.2  0.13  0.15      33   302.3   280.4  0.14  0.17
 0.082     676  99.58   300.2   285.2  0.13  0.16      41   287.0   262.1  0.19  0.23
 0.097     737  99.87   254.4   241.6  0.15  0.16      38   275.2   253.1  0.16  0.19
 0.112     771  99.64   208.9   201.3  0.15  0.16      53   212.3   195.2  0.20  0.21
 0.127     831  99.77   180.4   175.4  0.17  0.18      44   207.1   191.1  0.18  0.21
 0.142     868  99.78   163.4   159.9  0.17  0.17      47   148.0   150.6  0.22  0.24
 0.156     940  99.60   152.5   149.1  0.16  0.17      51   135.0   136.7  0.17  0.18
 0.171     934  99.20   133.5   131.4  0.17  0.17      60   127.3   122.6  0.25  0.25
 0.186     995  99.15   126.0   123.9  0.16  0.16      55   122.8   124.3  0.22  0.22
 0.201    1029  99.00   118.8   115.5  0.16  0.15      58   121.1   115.5  0.21  0.21
 0.216    1043  98.30   113.7   110.2  0.16  0.15      55    95.2    97.9  0.23  0.22
 0.231    1083  97.76   100.6   100.0  0.17  0.15      53    99.3    91.9  0.21  0.20
 0.246    1132  97.54    95.9    94.7  0.15  0.14      59   102.2   105.4  0.22  0.21
 0.260    1128  96.73    85.2    86.7  0.17  0.16      54    83.2    86.2  0.20  0.18
 0.275    1144  93.70    73.1    75.7  0.18  0.15      61    71.5    78.6  0.25  0.21
 0.290     758  61.35    58.6    69.2  0.30  0.23      34    53.6    72.0  0.44  0.29
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    6. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    6. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0078   131   0.939   112   0.832   243   0.889  1.019
  0.0227   270   0.902   114   0.811   384   0.875  1.014
  0.0375   359   0.916   118   0.856   477   0.901  1.009
  0.0524   438   0.947   106   0.899   544   0.937  1.004
  0.0673   500   0.946   112   0.851   612   0.928  0.999
  0.0821   565   0.941   111   0.864   676   0.929  0.994
  0.0970   623   0.926   114   0.868   737   0.917  0.989
  0.1118   657   0.916   114   0.835   771   0.904  0.984
  0.1267   717   0.900   114   0.837   831   0.891  0.979
  0.1416   759   0.887   109   0.829   868   0.880  0.974
  0.1564   823   0.888   117   0.837   940   0.882  0.969
  0.1713   825   0.880   109   0.804   934   0.871  0.964
  0.1861   882   0.881   113   0.789   995   0.871  0.959
  0.2010   919   0.877   110   0.857  1029   0.875  0.954
  0.2158   936   0.879   107   0.804  1043   0.872  0.950
  0.2307   982   0.869   101   0.775  1083   0.860  0.945
  0.2456  1021   0.877   111   0.818  1132   0.871  0.940
  0.2604  1032   0.861    96   0.811  1128   0.857  0.935
  0.2753  1046   0.843    98   0.775  1144   0.837  0.931
  0.2901   719   0.822    39   0.847   758   0.823  0.926
 $$
Resolution limits                    =     50.000     1.833
Number of used reflections           =      16329
Percentage observed                  =    95.7230
Percentage of free reflections       =     5.1246
Overall R factor                     =     0.1555
Free R factor                        =     0.1904
Overall weighted R factor            =     0.1656
Free weighted R factor               =     0.2075
Overall correlation coefficient      =     0.9654
Free correlation coefficient         =     0.9501
Cruickshanks DPI for coordinate error=     0.1259
DPI based on free R factor           =     0.1171
Overall figure of merit              =     0.8788
ML based su of positional parameters =     0.0754
ML based su of thermal parameters    =     2.4975
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.20
             Elapsed =           0.00
 
    **** Things for loggraph, R factor and others vs cycle  ****
 
 
$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LLG vs cycle :N:1,5:
:Geometry vs cycle:N:1,6,7,8:
$$
      Ncyc   Rfact   Rfree     FOM         LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
         0   0.228   0.221    0.851       88700.2    0.028    4.533    0.163
         1   0.184   0.201    0.872       85078.6    0.029    2.509    0.178
         2   0.169   0.195    0.878       83708.6    0.030    2.448    0.194
         3   0.162   0.193    0.879       83089.2    0.031    2.431    0.200
         4   0.158   0.192    0.879       82787.4    0.031    2.404    0.202
         5   0.155   0.190    0.879       82619.6    0.031    2.378    0.202
 $$

 Refmac_5.3.0040:  End of Refmac_5.3.0040
Times: User:      14.7s System:    0.8s Elapsed:     0:16
*************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final coordinates (XYZOUT) to /home/pjx/PROJECTS/myProject/rnase_refmac4.pdb *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final phases (HKLOUT) to /home/pjx/PROJECTS/myProject/rnase18_refmac4.mtz *************************************************************************** #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 17 Jul 2007 11:42:35 #CCP4I TERMINATION OUTPUT_FILES /home/pjx/PROJECTS/myProject/PROJECT_156_NATIVE.refmac.cif PROJECT #CCP4I MESSAGE Task completed successfully