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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:02:56 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

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

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "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

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 10
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R10_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R10_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R10_1-60A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/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 will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links 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


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:    10
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.6000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 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)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

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
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R10_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.047 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.203 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.831 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.189 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.421 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.384 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.088 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 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     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           10
Number of "free" reflections       1418
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.899 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.31615663    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                40.2
Norm of Geom. positional gradient                82.1
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                 0.226E+05
Product of X_ray and Geom posit. gradients     -0.153E+08
 Cosine of angle between them                      -0.477
Product of X_ray and Geom B-fact gradients     -0.412E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8710E+06 GEOM=     0.2745E+05 TOTAL=     0.8985E+06
 function value    898489.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.840     1.644
Bond angles  : others                          3242     2.353     1.582
Torsion angles, period  1. refined              184     6.804     5.000
Torsion angles, period  2. refined               90    35.671    22.778
Torsion angles, period  3. refined              268    13.121    15.000
Torsion angles, period  4. refined                9    11.328    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.018     0.020
VDW repulsions: refined_atoms                   311     0.266     0.200
VDW repulsions.others                          1322     0.234     0.200
VDW; torsion: refined_atoms                     724     0.172     0.200
VDW; torsion.others                             707     0.082     0.200
HBOND: refined_atoms                            236     0.190     0.200
HBOND.others                                      1     0.003     0.200
VDW repulsions: symmetry: refined_atoms          11     0.188     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   23     0.202     0.200
M. chain bond B values: refined atoms           745     1.710     1.382
M. chain bond B values: others                  745     1.707     1.382
M. chain angle B values: refined atoms          926     2.647     2.056
M. chain angle B values: others                 927     2.646     2.056
S. chain bond B values: refined atoms           811     3.051     1.778
S. chain bond B values: others                  810     3.043     1.778
S. chain angle B values: refined atoms         1177     4.670     2.501
S. chain angle B values: others                1178     4.668     2.501
Long range B values: refined atoms             1869     6.992    19.669
Long range B values: others                    1769     6.693    18.126
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    1.2543
Partial structure    1: scale =     0.3852, B  =   48.4307
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3592 100.00   432.8   443.1  0.17  0.18     190   424.4   430.0  0.21  0.22
 0.147    6121  99.97   258.4   243.5  0.16  0.14     323   265.2   247.8  0.20  0.18
 0.244    7795 100.00   167.5   152.1  0.18  0.16     423   163.0   149.7  0.22  0.19
 0.342    9108 100.00    71.2    85.9  0.34  0.27     482    73.5    86.7  0.35  0.28
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.904    971   0.791   3592   0.873  0.945  0.9560  0.9667  0.8843  0.9335
  0.1468   5133   0.891    988   0.798   6121   0.876  1.027  0.9543  0.9637  0.9150  0.9439
  0.2444   6804   0.871    991   0.768   7795   0.858  1.052  0.9458  0.9577  0.8990  0.9399
  0.3419   8144   0.667    969   0.588   9113   0.658  0.700  0.8646  0.8644  0.8166  0.8504
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26620
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0574
Overall R factor                     =     0.1924
Free R factor                        =     0.2288
Average Fourier shell correlation    =     0.9284
AverageFree Fourier shell correlation=     0.9215
Overall weighted R factor            =     0.1677
Free weighted R factor               =     0.2018
Overall weighted R2 factor           =     0.2014
Free weighted R2 factor              =     0.2470
Average correlation coefficient      =     0.9094
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9364
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.0978
Overall figure of merit              =     0.7958
ML based su of positional parameters =     0.0695
ML based su of thermal parameters    =     2.1040
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134013.91       27445.730       898489.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38369653    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874768.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0557
Partial structure    1: scale =     0.3875, B  =   47.8322
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2285
Average Fourier shell correlation    =     0.9400
AverageFree Fourier shell correlation=     0.9320
Average correlation coefficient      =     0.9103
Overall figure of merit              =     0.8298
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133044.05       10028.137       874768.19       898489.56    


     CGMAT cycle number =      3

 Weight matrix   0.39879599    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872280.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0227
Partial structure    1: scale =     0.3866, B  =   43.9192
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2281
Average Fourier shell correlation    =     0.9427
AverageFree Fourier shell correlation=     0.9340
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8372
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132764.11       9359.7490       872280.31       874768.19    


     CGMAT cycle number =      4

 Weight matrix   0.40105081    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871513.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0157
Partial structure    1: scale =     0.3880, B  =   43.3624
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1914
Free R factor                        =     0.2280
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8384
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132672.03       9191.7383       871513.81       872280.31    


     CGMAT cycle number =      5

 Weight matrix   0.40115824    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871340.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0040
Partial structure    1: scale =     0.3888, B  =   43.3336
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1914
Free R factor                        =     0.2281
Average Fourier shell correlation    =     0.9434
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8384
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132641.95       9213.8945       871340.44       871513.81    


     CGMAT cycle number =      6

 Weight matrix   0.40162435    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871288.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0005
Partial structure    1: scale =     0.3887, B  =   43.3273
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1914
Free R factor                        =     0.2282
Average Fourier shell correlation    =     0.9435
AverageFree Fourier shell correlation=     0.9346
Average correlation coefficient      =     0.9141
Overall figure of merit              =     0.8384
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132630.06       9239.4297       871288.75       871340.44    


     CGMAT cycle number =      7

 Weight matrix   0.40294039    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871255.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0212
Partial structure    1: scale =     0.3873, B  =   43.1269
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9436
AverageFree Fourier shell correlation=     0.9347
Average correlation coefficient      =     0.9142
Overall figure of merit              =     0.8387
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132624.25       9244.0928       871255.56       871288.75    


     CGMAT cycle number =      8

 Weight matrix   0.36655676    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    792865.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0126
Partial structure    1: scale =     0.3868, B  =   42.8500
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9347
Average correlation coefficient      =     0.9143
Overall figure of merit              =     0.8388
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    132616.61       9263.5742       792865.25       871255.56    


     CGMAT cycle number =      9

 Weight matrix   0.33237442    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721634.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0127
Partial structure    1: scale =     0.3867, B  =   42.7709
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9435
AverageFree Fourier shell correlation=     0.9347
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8387
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132671.64       8973.5137       721634.25       792865.25    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.909 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.33137605    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                39.0
Norm of X_ray B-factor gradient                  105.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.371E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7131E+06 GEOM=      8632.     TOTAL=     0.7217E+06
 function value    721703.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.797     1.644
Bond angles  : others                          3242     1.500     1.582
Torsion angles, period  1. refined              184     6.763     5.000
Torsion angles, period  2. refined               90    35.277    22.778
Torsion angles, period  3. refined              268    12.809    15.000
Torsion angles, period  4. refined                9    11.366    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.266     0.200
VDW repulsions.others                          1357     0.206     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             785     0.084     0.200
HBOND: refined_atoms                            233     0.191     0.200
HBOND.others                                      1     0.050     0.200
VDW repulsions: symmetry: refined_atoms          10     0.200     0.200
VDW repulsions: symmetry: others                 26     0.176     0.200
HBOND: symmetry: refined_atoms                   25     0.184     0.200
M. chain bond B values: refined atoms           745     1.688     1.507
M. chain bond B values: others                  745     1.684     1.507
M. chain angle B values: refined atoms          926     2.633     2.247
M. chain angle B values: others                 927     2.632     2.247
S. chain bond B values: refined atoms           811     2.961     1.895
S. chain bond B values: others                  810     2.954     1.895
S. chain angle B values: refined atoms         1177     4.552     2.682
S. chain angle B values: others                1178     4.550     2.681
Long range B values: refined atoms             1866     6.815    21.248
Long range B values: others                    1767     6.503    19.690
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0147
Partial structure    1: scale =     0.3866, B  =   42.6642
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3592 100.00   433.1   443.4  0.17  0.18     190   424.7   429.5  0.21  0.22
 0.147    6121  99.97   258.5   243.5  0.16  0.15     323   265.3   247.9  0.20  0.18
 0.244    7795 100.00   167.6   151.9  0.19  0.16     423   163.1   149.6  0.22  0.19
 0.342    9108 100.00    71.3    85.5  0.32  0.26     482    73.6    86.0  0.34  0.27
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.915    971   0.808   3592   0.886  0.946  0.9597  0.9692  0.8849  0.9330
  0.1468   5133   0.894    988   0.800   6121   0.879  1.027  0.9547  0.9639  0.9143  0.9420
  0.2444   6804   0.883    991   0.782   7795   0.870  1.054  0.9507  0.9612  0.8999  0.9383
  0.3419   8144   0.774    969   0.695   9113   0.766  0.750  0.8969  0.9039  0.8260  0.8652
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26620
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0574
Overall R factor                     =     0.1925
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9345
Overall weighted R factor            =     0.1686
Free weighted R factor               =     0.2025
Overall weighted R2 factor           =     0.2024
Free weighted R2 factor              =     0.2477
Average correlation coefficient      =     0.9134
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9369
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.0977
Overall figure of merit              =     0.8385
ML based su of positional parameters =     0.0617
ML based su of thermal parameters    =     1.8179
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132751.09       8632.1641       721753.38       721634.25    

 fvalues    132751.09       8632.1641       721739.63       721719.75    
 fvalues    132751.09       8632.1641       721739.63       721719.75    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.909 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R10_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.794     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.763     5.000
Torsion angles, period  2. refined               90    35.269    22.778
Torsion angles, period  3. refined              268    12.803    15.000
Torsion angles, period  4. refined                9    11.359    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.266     0.200
VDW repulsions.others                          1358     0.206     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             784     0.084     0.200
HBOND: refined_atoms                            232     0.191     0.200
HBOND.others                                      1     0.050     0.200
VDW repulsions: symmetry: refined_atoms          10     0.200     0.200
VDW repulsions: symmetry: others                 26     0.176     0.200
HBOND: symmetry: refined_atoms                   25     0.184     0.200
M. chain bond B values: refined atoms           745     1.685     1.507
M. chain bond B values: others                  745     1.681     1.507
M. chain angle B values: refined atoms          926     2.629     2.247
M. chain angle B values: others                 927     2.628     2.247
S. chain bond B values: refined atoms           811     2.953     1.894
S. chain bond B values: others                  810     2.947     1.894
S. chain angle B values: refined atoms         1177     4.541     2.681
S. chain angle B values: others                1178     4.539     2.680
Long range B values: refined atoms             1865     6.808    21.235
Long range B values: others                    1766     6.496    19.676
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0145
Partial structure    1: scale =     0.3865, B  =   42.5609
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3592 100.00   433.1   443.4  0.17  0.18     190   424.7   429.5  0.21  0.22
 0.147    6121  99.97   258.6   243.5  0.16  0.15     323   265.4   247.9  0.21  0.18
 0.244    7795 100.00   167.7   151.9  0.19  0.16     423   163.1   149.6  0.22  0.19
 0.342    9108 100.00    71.3    85.5  0.32  0.26     482    73.6    86.0  0.34  0.27
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.915    971   0.808   3592   0.886  0.946  0.9597  0.9692  0.8849  0.9330
  0.1468   5133   0.894    988   0.800   6121   0.879  1.027  0.9547  0.9639  0.9143  0.9420
  0.2444   6804   0.883    991   0.782   7795   0.870  1.054  0.9507  0.9612  0.8999  0.9383
  0.3419   8144   0.774    969   0.695   9113   0.766  0.750  0.8969  0.9039  0.8261  0.8651
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26620
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0574
Overall R factor                     =     0.1925
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9345
Overall weighted R factor            =     0.1687
Free weighted R factor               =     0.2025
Overall weighted R2 factor           =     0.2025
Free weighted R2 factor              =     0.2478
Average correlation coefficient      =     0.9134
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9369
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.0977
Overall figure of merit              =     0.8385
ML based su of positional parameters =     0.0617
ML based su of thermal parameters    =     1.8179
-----------------------------------------------------------------------------
  Time in seconds: CPU =        18.80
             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:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1924   0.2288   0.796      134014.    7311.2   0.0131  0.986   1.840  1.072   0.091
       1   0.1926   0.2285   0.830      133044.    7276.0   0.0123  0.928   1.794  1.045   0.088
       2   0.1917   0.2281   0.837      132764.    7266.8   0.0130  0.984   1.822  1.062   0.089
       3   0.1914   0.2280   0.838      132672.    7264.3   0.0132  0.995   1.839  1.072   0.090
       4   0.1914   0.2281   0.838      132642.    7263.6   0.0132  0.999   1.849  1.078   0.090
       5   0.1914   0.2282   0.838      132630.    7263.0   0.0132  0.999   1.855  1.081   0.090
       6   0.1916   0.2283   0.839      132624.    7263.3   0.0132  1.001   1.859  1.083   0.091
       7   0.1916   0.2283   0.839      132617.    7262.7   0.0132  1.002   1.862  1.085   0.091
       8   0.1920   0.2283   0.839      132672.    7263.6   0.0127  0.959   1.834  1.068   0.089
       9   0.1925   0.2286   0.838      132748.    7265.4   0.0121  0.914   1.797  1.046   0.087
      10   0.1925   0.2286   0.838      132757.    7265.6   0.0120  0.912   1.794  1.045   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1924   0.1925
             R free    0.2288   0.2286
     Rms BondLength    0.0131   0.0120
      Rms BondAngle    1.8405   1.7938
     Rms ChirVolume    0.0908   0.0866
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.0s System:    0.2s Elapsed:     0:51