###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:19:48 


 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 14
  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_R14_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R14_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_R14_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:    14
  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_R14_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=   2.038 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=   2.196 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=   1.825 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=   2.219 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=   2.436 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=   2.386 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=   2.095 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                           14
Number of "free" reflections       1344
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.= 0.889 id.= 3.000 dev= -2.11 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   0.31706449    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.4
Norm of Geom. positional gradient                79.5
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.440
Product of X_ray and Geom B-fact gradients     -0.416E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8735E+06 GEOM=     0.2599E+05 TOTAL=     0.8995E+06
 function value    899533.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.786     1.644
Bond angles  : others                          3242     2.347     1.582
Torsion angles, period  1. refined              184     6.866     5.000
Torsion angles, period  2. refined               90    36.235    22.778
Torsion angles, period  3. refined              268    13.860    15.000
Torsion angles, period  4. refined                9    11.872    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1337     0.230     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             719     0.081     0.200
HBOND: refined_atoms                            227     0.196     0.200
HBOND.others                                      1     0.047     0.200
VDW repulsions: symmetry: refined_atoms          10     0.195     0.200
VDW repulsions: symmetry: others                 24     0.183     0.200
HBOND: symmetry: refined_atoms                   20     0.209     0.200
M. chain bond B values: refined atoms           745     1.652     1.390
M. chain bond B values: others                  745     1.650     1.390
M. chain angle B values: refined atoms          926     2.628     2.068
M. chain angle B values: others                 927     2.627     2.068
S. chain bond B values: refined atoms           811     2.952     1.787
S. chain bond B values: others                  810     2.946     1.786
S. chain angle B values: refined atoms         1177     4.580     2.515
S. chain angle B values: others                1178     4.578     2.514
Long range B values: refined atoms             1854     7.144    19.611
Long range B values: others                    1757     6.844    18.048
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2313
Partial structure    1: scale =     0.3874, B  =   47.6419
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3601 100.00   431.2   440.8  0.17  0.18     181   467.6   468.9  0.18  0.19
 0.147    6140  99.97   258.5   243.6  0.17  0.15     304   269.3   250.6  0.19  0.17
 0.244    7811 100.00   167.6   151.7  0.19  0.17     407   165.1   151.7  0.22  0.19
 0.342    9138 100.00    71.2    85.9  0.34  0.27     452    75.4    90.2  0.33  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2632   0.918    969   0.825   3601   0.893  0.948  0.9723  0.9707  0.9379  0.9337
  0.1468   5160   0.890    980   0.792   6140   0.874  1.027  0.9590  0.9632  0.9205  0.9414
  0.2444   6821   0.869    990   0.766   7811   0.856  1.054  0.9479  0.9570  0.9097  0.9372
  0.3419   8148   0.668    995   0.586   9143   0.659  0.701  0.8676  0.8654  0.8438  0.8485
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26694
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.7935
Overall R factor                     =     0.1941
Free R factor                        =     0.2113
Average Fourier shell correlation    =     0.9289
AverageFree Fourier shell correlation=     0.9267
Overall weighted R factor            =     0.1680
Free weighted R factor               =     0.1873
Overall weighted R2 factor           =     0.1997
Free weighted R2 factor              =     0.2177
Average correlation coefficient      =     0.9073
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9535
Cruickshanks DPI for coordinate error=     0.0973
DPI based on free R factor           =     0.0901
Overall figure of merit              =     0.7979
ML based su of positional parameters =     0.0694
ML based su of thermal parameters    =     2.1069
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134398.66       25989.207       899533.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38395488    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    877192.00    

-------------------------------------------------------------------------------
             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  =   -0.0577
Partial structure    1: scale =     0.3883, B  =   47.5753
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2105
Average Fourier shell correlation    =     0.9390
AverageFree Fourier shell correlation=     0.9366
Average correlation coefficient      =     0.9091
Overall figure of merit              =     0.8265
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133426.20       9968.0732       877192.00       899533.75    


     CGMAT cycle number =      3

 Weight matrix   0.39718905    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874565.63    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0168
Partial structure    1: scale =     0.3890, B  =   43.5507
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2097
Average Fourier shell correlation    =     0.9419
AverageFree Fourier shell correlation=     0.9391
Average correlation coefficient      =     0.9112
Overall figure of merit              =     0.8343
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    133097.00       9481.3457       874565.63       877192.00    


     CGMAT cycle number =      4

 Weight matrix   0.36333707    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    795233.13    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0125
Partial structure    1: scale =     0.3892, B  =   43.1129
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1921
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9397
Average correlation coefficient      =     0.9121
Overall figure of merit              =     0.8359
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    133000.33       9364.1133       795233.13       874565.63    


     CGMAT cycle number =      5

 Weight matrix   0.33055964    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723606.69    

-------------------------------------------------------------------------------
             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  =   -0.0035
Partial structure    1: scale =     0.3902, B  =   43.0795
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9427
AverageFree Fourier shell correlation=     0.9399
Average correlation coefficient      =     0.9121
Overall figure of merit              =     0.8361
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    133011.73       9119.0342       723606.69       795233.13    


     CGMAT cycle number =      6

 Weight matrix   0.33033079    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723575.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0036
Partial structure    1: scale =     0.3902, B  =   43.0180
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9398
Average correlation coefficient      =     0.9118
Overall figure of merit              =     0.8361
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    133063.83       8807.8164       723575.25       723606.69    


     CGMAT cycle number =      7

 Weight matrix   0.33005333    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723584.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0037
Partial structure    1: scale =     0.3903, B  =   42.8800
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1930
Free R factor                        =     0.2089
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9398
Average correlation coefficient      =     0.9118
Overall figure of merit              =     0.8360
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    133081.19       8731.4170       723616.13       723575.25    

 fvalues    133081.19       8731.4170       723611.44       723592.13    
 fvalues    133081.19       8731.4170       723611.44       723592.13    


     CGMAT cycle number =      8

 Weight matrix   0.32990074    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723598.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0021
Partial structure    1: scale =     0.3902, B  =   42.8486
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1930
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9398
Average correlation coefficient      =     0.9118
Overall figure of merit              =     0.8360
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    133085.66       8719.5938       723612.06       723592.13    

 fvalues    133085.66       8719.5938       723609.38       723604.25    
 fvalues    133085.66       8719.5938       723609.38       723604.25    


     CGMAT cycle number =      9

 Weight matrix   0.32989281    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723609.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0031
Partial structure    1: scale =     0.3900, B  =   42.8094
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1930
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9398
Average correlation coefficient      =     0.9118
Overall figure of merit              =     0.8360
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    133087.64       8716.6592       723618.19       723604.25    

 fvalues    133087.64       8716.6592       723613.69       723612.06    
 fvalues    133087.64       8716.6592       723613.69       723612.06    


     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.= 0.895 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   0.32993716    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.9
Norm of Geom. positional gradient                39.0
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.147E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.383E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7149E+06 GEOM=      8715.     TOTAL=     0.7236E+06
 function value    723618.00    

-------------------------------------------------------------------------------
             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     1.794     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.851     5.000
Torsion angles, period  2. refined               90    35.915    22.778
Torsion angles, period  3. refined              268    13.774    15.000
Torsion angles, period  4. refined                9    12.097    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.265     0.200
VDW repulsions.others                          1373     0.205     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             768     0.084     0.200
HBOND: refined_atoms                            220     0.202     0.200
HBOND.others                                      1     0.106     0.200
VDW repulsions: symmetry: refined_atoms           9     0.204     0.200
VDW repulsions: symmetry: others                 24     0.177     0.200
HBOND: symmetry: refined_atoms                   22     0.182     0.200
M. chain bond B values: refined atoms           745     1.705     1.509
M. chain bond B values: others                  745     1.702     1.509
M. chain angle B values: refined atoms          926     2.695     2.249
M. chain angle B values: others                 927     2.693     2.249
S. chain bond B values: refined atoms           811     3.074     1.914
S. chain bond B values: others                  810     3.068     1.914
S. chain angle B values: refined atoms         1177     4.724     2.703
S. chain angle B values: others                1178     4.722     2.703
Long range B values: refined atoms             1855     7.147    21.077
Long range B values: others                    1761     6.811    19.581
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0048
Partial structure    1: scale =     0.3899, B  =   42.7988
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3601 100.00   431.1   440.8  0.17  0.18     181   467.4   468.7  0.17  0.19
 0.147    6140  99.97   258.5   243.3  0.17  0.15     304   269.2   250.9  0.19  0.17
 0.244    7811 100.00   167.6   151.8  0.19  0.17     407   165.1   151.7  0.22  0.18
 0.342    9138 100.00    71.2    85.5  0.33  0.26     452    75.4    90.0  0.33  0.26
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2632   0.928    969   0.837   3601   0.903  0.948  0.9745  0.9729  0.9393  0.9334
  0.1468   5160   0.897    980   0.800   6140   0.881  1.027  0.9608  0.9648  0.9212  0.9416
  0.2444   6821   0.883    990   0.782   7811   0.870  1.054  0.9530  0.9614  0.9124  0.9373
  0.3419   8148   0.759    995   0.672   9143   0.750  0.741  0.9000  0.8995  0.8482  0.8615
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26694
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.7935
Overall R factor                     =     0.1930
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9398
Overall weighted R factor            =     0.1678
Free weighted R factor               =     0.1848
Overall weighted R2 factor           =     0.1999
Free weighted R2 factor              =     0.2157
Average correlation coefficient      =     0.9118
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9543
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.0891
Overall figure of merit              =     0.8360
ML based su of positional parameters =     0.0618
ML based su of thermal parameters    =     1.8448
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    133090.03       8715.4775       723621.88       723612.06    
 fvalues    133090.03       8715.4775       723621.88       723623.69    

    ****                              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.= 0.895 id.= 3.000 dev= -2.10 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_R14_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     1.501     1.582
Torsion angles, period  1. refined              184     6.851     5.000
Torsion angles, period  2. refined               90    35.912    22.778
Torsion angles, period  3. refined              268    13.774    15.000
Torsion angles, period  4. refined                9    12.097    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.265     0.200
VDW repulsions.others                          1374     0.204     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             771     0.084     0.200
HBOND: refined_atoms                            220     0.202     0.200
HBOND.others                                      1     0.106     0.200
VDW repulsions: symmetry: refined_atoms           9     0.204     0.200
VDW repulsions: symmetry: others                 24     0.177     0.200
HBOND: symmetry: refined_atoms                   22     0.181     0.200
M. chain bond B values: refined atoms           745     1.705     1.509
M. chain bond B values: others                  745     1.702     1.509
M. chain angle B values: refined atoms          926     2.694     2.249
M. chain angle B values: others                 927     2.693     2.249
S. chain bond B values: refined atoms           811     3.073     1.914
S. chain bond B values: others                  810     3.068     1.914
S. chain angle B values: refined atoms         1177     4.723     2.703
S. chain angle B values: others                1178     4.721     2.703
Long range B values: refined atoms             1855     7.147    21.076
Long range B values: others                    1761     6.810    19.581
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0037
Partial structure    1: scale =     0.3899, B  =   42.8044
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3601 100.00   431.1   440.8  0.17  0.18     181   467.5   468.7  0.17  0.19
 0.147    6140  99.97   258.5   243.3  0.17  0.15     304   269.2   250.9  0.19  0.17
 0.244    7811 100.00   167.6   151.7  0.19  0.17     407   165.1   151.7  0.22  0.18
 0.342    9138 100.00    71.2    85.5  0.33  0.26     452    75.4    90.0  0.33  0.26
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2632   0.928    969   0.837   3601   0.903  0.948  0.9745  0.9729  0.9392  0.9334
  0.1468   5160   0.897    980   0.800   6140   0.881  1.027  0.9608  0.9648  0.9212  0.9416
  0.2444   6821   0.883    990   0.782   7811   0.870  1.054  0.9530  0.9614  0.9124  0.9372
  0.3419   8148   0.759    995   0.672   9143   0.749  0.741  0.8999  0.8994  0.8482  0.8615
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26694
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.7935
Overall R factor                     =     0.1930
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9398
Overall weighted R factor            =     0.1678
Free weighted R factor               =     0.1849
Overall weighted R2 factor           =     0.2000
Free weighted R2 factor              =     0.2157
Average correlation coefficient      =     0.9118
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9543
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.0891
Overall figure of merit              =     0.8360
ML based su of positional parameters =     0.0618
ML based su of thermal parameters    =     1.8448
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.19
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1941   0.2113   0.798      134399.    6928.9   0.0121  0.911   1.786  1.034   0.088
       1   0.1936   0.2105   0.827      133426.    6899.9   0.0123  0.929   1.788  1.037   0.090
       2   0.1924   0.2097   0.834      133097.    6890.5   0.0133  1.000   1.834  1.065   0.092
       3   0.1921   0.2093   0.836      133000.    6887.4   0.0134  1.011   1.856  1.078   0.092
       4   0.1924   0.2090   0.836      133012.    6886.4   0.0128  0.970   1.839  1.067   0.091
       5   0.1929   0.2088   0.836      133064.    6886.5   0.0122  0.927   1.806  1.048   0.088
       6   0.1930   0.2089   0.836      133080.    6887.4   0.0122  0.922   1.796  1.042   0.088
       7   0.1930   0.2088   0.836      133085.    6887.5   0.0122  0.922   1.795  1.042   0.088
       8   0.1930   0.2088   0.836      133087.    6887.6   0.0122  0.922   1.794  1.041   0.088
       9   0.1930   0.2088   0.836      133089.    6887.7   0.0122  0.921   1.794  1.041   0.088
      10   0.1930   0.2088   0.836      133091.    6887.8   0.0122  0.921   1.794  1.041   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1941   0.1930
             R free    0.2113   0.2088
     Rms BondLength    0.0121   0.0122
      Rms BondAngle    1.7862   1.7941
     Rms ChirVolume    0.0880   0.0878
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.5s System:    0.2s Elapsed:     0:56