###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:40:01 


 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 1.68     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 0
  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_step0-01A_R00_1-69A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-68A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-68A.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       0.0886
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6800
  Estimated number of reflections :      31298
  Free R exclusion - flag equals:     0
  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  1.6800

  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_step0-01A_R00_1-69A.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=   2.043 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=   2.207 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=   1.833 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=   2.235 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=   2.411 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=   2.396 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=   2.124 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:22-OCT-19
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            0
Number of "free" reflections       1243
Number of   all  reflections      24341
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          24341

   Current auto weighting coefficient =    6.6995921    

 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.= 0.901 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        :   120  120  256
 Maximuum H,K,L                 :    35   35   73
 Minimum acceptable grid spacing:    80   80  168
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   73
 Minimum acceptable grid spacing:    80   80  168
 Weight matrix   0.29487130    
 Actual weight    6.6995921      is applied to the X-ray term
Norm of X_ray positional gradient                36.9
Norm of Geom. positional gradient                81.8
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.474
Product of X_ray and Geom B-fact gradients     -0.386E+08
 Cosine of angle between them                      -0.895


Residuals: XRAY=     0.7987E+06 GEOM=     0.1372E+05 TOTAL=     0.8124E+06
 function value    812395.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.838     1.644
Bond angles  : others                          3238     2.364     1.580
Torsion angles, period  1. refined              185     6.815     5.000
Torsion angles, period  2. refined               90    35.113    22.778
Torsion angles, period  3. refined              268    13.627    15.000
Torsion angles, period  4. refined                9    12.215    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   297     0.247     0.200
VDW repulsions.others                          1318     0.220     0.200
VDW; torsion: refined_atoms                     717     0.175     0.200
VDW; torsion.others                             725     0.081     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.091     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 22     0.201     0.200
HBOND: symmetry: refined_atoms                   21     0.179     0.200
M. chain bond B values: refined atoms           746     1.717     1.404
M. chain bond B values: others                  746     1.714     1.404
M. chain angle B values: refined atoms          929     2.678     2.094
M. chain angle B values: others                 930     2.677     2.094
S. chain bond B values: refined atoms           811     3.061     1.806
S. chain bond B values: others                  810     3.055     1.805
S. chain angle B values: refined atoms         1177     4.707     2.540
S. chain angle B values: others                1178     4.705     2.539
Long range B values: refined atoms             1837     7.128    19.416
Long range B values: others                    1747     6.877    18.040
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0885
Partial structure    1: scale =     0.3873, B  =   43.5366
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.045    3150 100.00   449.8   459.7  0.16  0.17     140   443.3   455.1  0.20  0.21
 0.133    5297 100.00   289.0   275.8  0.17  0.15     304   295.8   274.1  0.22  0.20
 0.222    6731  99.97   195.5   178.5  0.17  0.15     375   202.7   187.4  0.20  0.17
 0.310    7908 100.00    96.5   109.3  0.26  0.20     424    91.4   105.9  0.32  0.25
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0448   2263   0.913    887   0.816   3150   0.885  0.950  0.9613  0.9703  0.9043  0.9402
  0.1332   4414   0.872    883   0.764   5297   0.854  1.002  0.9466  0.9585  0.8955  0.9412
  0.2217   5844   0.880    887   0.768   6731   0.865  1.051  0.9557  0.9604  0.9146  0.9419
  0.3101   7026   0.758    892   0.684   7918   0.750  0.807  0.8986  0.9175  0.8522  0.9018
 $$
Resolution limits                    =     41.964     1.680
Number of used reflections           =      23096
Percentage observed                  =    99.9877
Percentage of free reflections       =     5.1070
Overall R factor                     =     0.1804
Free R factor                        =     0.2254
Average Fourier shell correlation    =     0.9466
AverageFree Fourier shell correlation=     0.9346
Overall weighted R factor            =     0.1603
Free weighted R factor               =     0.1995
Overall weighted R2 factor           =     0.1916
Free weighted R2 factor              =     0.2356
Average correlation coefficient      =     0.9278
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9330
Cruickshanks DPI for coordinate error=     0.1053
DPI based on free R factor           =     0.1086
Overall figure of merit              =     0.8257
ML based su of positional parameters =     0.0731
ML based su of thermal parameters    =     2.2404
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    119212.10       13723.245       812395.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35933363    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    802029.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =   -0.0704
Partial structure    1: scale =     0.3872, B  =   43.4855
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1805
Free R factor                        =     0.2247
Average Fourier shell correlation    =     0.9532
AverageFree Fourier shell correlation=     0.9421
Average correlation coefficient      =     0.9272
Overall figure of merit              =     0.8523
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    118413.27       8709.1426       802029.69       812395.69    


     CGMAT cycle number =      3

 Weight matrix   0.36470601    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801523.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =   -0.0178
Partial structure    1: scale =     0.3871, B  =   43.3737
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1801
Free R factor                        =     0.2247
Average Fourier shell correlation    =     0.9538
AverageFree Fourier shell correlation=     0.9426
Average correlation coefficient      =     0.9283
Overall figure of merit              =     0.8542
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    118283.55       9071.9502       801523.44       802029.69    


     CGMAT cycle number =      4

 Weight matrix   0.36553028    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801423.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0013
Partial structure    1: scale =     0.3873, B  =   43.3817
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1802
Free R factor                        =     0.2249
Average Fourier shell correlation    =     0.9539
AverageFree Fourier shell correlation=     0.9427
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    118252.32       9181.0039       801423.31       801523.44    


     CGMAT cycle number =      5

 Weight matrix   0.36587244    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801382.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0007
Partial structure    1: scale =     0.3874, B  =   43.3737
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1802
Free R factor                        =     0.2249
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9427
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8545
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    118241.53       9212.8125       801382.81       801423.31    


     CGMAT cycle number =      6

 Weight matrix   0.36580673    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801350.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0048
Partial structure    1: scale =     0.3875, B  =   43.3075
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1803
Free R factor                        =     0.2249
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9428
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8545
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    118234.95       9224.3164       801350.25       801382.81    


     CGMAT cycle number =      7

 Weight matrix   0.36583513    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801341.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0020
Partial structure    1: scale =     0.3875, B  =   43.3009
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1803
Free R factor                        =     0.2249
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9428
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8545
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    118233.90       9223.0537       801341.94       801350.25    


     CGMAT cycle number =      8

 Weight matrix   0.36556706    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801368.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0000
Partial structure    1: scale =     0.3875, B  =   43.3009
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1804
Free R factor                        =     0.2249
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9428
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    118238.14       9220.8086       801361.25       801341.94    
 fvalues    118238.14       9220.8086       801361.25       801368.13    


     CGMAT cycle number =      9

 Weight matrix   0.36528409    
 Actual weight    6.6995921      is applied to the X-ray term


 function value    801380.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0020
Partial structure    1: scale =     0.3876, B  =   43.2970
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1804
Free R factor                        =     0.2250
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9427
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    118241.09       9207.9922       801390.88       801368.13    

 fvalues    118241.09       9207.9922       801390.19       801375.13    
 fvalues    118241.09       9207.9922       801390.19       801375.13    


     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.= 0.920 id.= 3.000 dev= -2.08 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        :   120  120  256
 Maximuum H,K,L                 :    35   35   73
 Minimum acceptable grid spacing:    80   80  168
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   73
 Minimum acceptable grid spacing:    80   80  168
 Weight matrix   0.36503938    
 Actual weight    6.6995921      is applied to the X-ray term
Norm of X_ray positional gradient                42.9
Norm of Geom. positional gradient                42.9
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                  128.
Product of X_ray and Geom posit. gradients     -0.178E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.526E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7922E+06 GEOM=      9207.     TOTAL=     0.8014E+06
 function value    801394.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.846     1.644
Bond angles  : others                          3238     1.523     1.580
Torsion angles, period  1. refined              185     6.801     5.000
Torsion angles, period  2. refined               90    35.091    22.778
Torsion angles, period  3. refined              268    13.456    15.000
Torsion angles, period  4. refined                9    12.351    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.247     0.200
VDW repulsions.others                          1363     0.192     0.200
VDW; torsion: refined_atoms                     723     0.174     0.200
VDW; torsion.others                             777     0.085     0.200
HBOND: refined_atoms                            214     0.203     0.200
HBOND.others                                      1     0.019     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 25     0.172     0.200
HBOND: symmetry: refined_atoms                   21     0.181     0.200
M. chain bond B values: refined atoms           746     1.718     1.412
M. chain bond B values: others                  746     1.715     1.413
M. chain angle B values: refined atoms          929     2.690     2.107
M. chain angle B values: others                 930     2.688     2.107
S. chain bond B values: refined atoms           811     3.074     1.815
S. chain bond B values: others                  810     3.068     1.814
S. chain angle B values: refined atoms         1177     4.724     2.553
S. chain angle B values: others                1178     4.722     2.553
Long range B values: refined atoms             1839     7.090    19.560
Long range B values: others                    1750     6.843    18.182
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0053
Partial structure    1: scale =     0.3877, B  =   43.2777
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.045    3150 100.00   450.0   460.2  0.16  0.17     140   443.5   455.4  0.21  0.21
 0.133    5297 100.00   289.2   275.8  0.17  0.15     304   295.9   274.1  0.22  0.20
 0.222    6731  99.97   195.6   178.6  0.17  0.15     375   202.8   187.7  0.20  0.17
 0.310    7908 100.00    96.6   109.4  0.26  0.20     424    91.5   105.9  0.32  0.25
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0448   2263   0.926    887   0.834   3150   0.900  0.952  0.9645  0.9730  0.9043  0.9398
  0.1332   4414   0.872    883   0.765   5297   0.854  1.002  0.9470  0.9588  0.8960  0.9413
  0.2217   5844   0.888    887   0.777   6731   0.874  1.051  0.9584  0.9629  0.9162  0.9419
  0.3101   7026   0.828    892   0.756   7918   0.820  0.826  0.9186  0.9355  0.8544  0.9045
 $$
Resolution limits                    =     41.964     1.680
Number of used reflections           =      23096
Percentage observed                  =    99.9877
Percentage of free reflections       =     5.1070
Overall R factor                     =     0.1804
Free R factor                        =     0.2250
Average Fourier shell correlation    =     0.9539
AverageFree Fourier shell correlation=     0.9427
Overall weighted R factor            =     0.1607
Free weighted R factor               =     0.1997
Overall weighted R2 factor           =     0.1923
Free weighted R2 factor              =     0.2360
Average correlation coefficient      =     0.9287
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9333
Cruickshanks DPI for coordinate error=     0.1053
DPI based on free R factor           =     0.1085
Overall figure of merit              =     0.8544
ML based su of positional parameters =     0.0656
ML based su of thermal parameters    =     1.9647
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    118244.00       9207.4756       801394.44       801375.13    

 fvalues    118244.00       9207.4756       801390.63       801394.06    
 fvalues    118244.00       9207.4756       801390.63       801394.06    

    ****                              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.= 0.920 id.= 3.000 dev= -2.08 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_step0-01A_R00_1-68A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.846     1.644
Bond angles  : others                          3238     1.523     1.580
Torsion angles, period  1. refined              185     6.801     5.000
Torsion angles, period  2. refined               90    35.091    22.778
Torsion angles, period  3. refined              268    13.449    15.000
Torsion angles, period  4. refined                9    12.351    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.247     0.200
VDW repulsions.others                          1360     0.192     0.200
VDW; torsion: refined_atoms                     723     0.174     0.200
VDW; torsion.others                             781     0.085     0.200
HBOND: refined_atoms                            214     0.203     0.200
HBOND.others                                      1     0.019     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 25     0.172     0.200
HBOND: symmetry: refined_atoms                   21     0.181     0.200
M. chain bond B values: refined atoms           746     1.718     1.412
M. chain bond B values: others                  746     1.715     1.413
M. chain angle B values: refined atoms          929     2.689     2.107
M. chain angle B values: others                 930     2.688     2.107
S. chain bond B values: refined atoms           811     3.074     1.815
S. chain bond B values: others                  810     3.068     1.814
S. chain angle B values: refined atoms         1177     4.723     2.553
S. chain angle B values: others                1178     4.721     2.553
Long range B values: refined atoms             1839     7.089    19.560
Long range B values: others                    1750     6.842    18.181
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0430, B  =    0.0007
Partial structure    1: scale =     0.3877, B  =   43.2808
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.045    3150 100.00   450.0   460.2  0.16  0.17     140   443.5   455.5  0.21  0.21
 0.133    5297 100.00   289.2   275.8  0.17  0.15     304   295.9   274.2  0.22  0.20
 0.222    6731  99.97   195.6   178.6  0.17  0.15     375   202.8   187.7  0.20  0.17
 0.310    7908 100.00    96.6   109.4  0.26  0.20     424    91.5   105.9  0.32  0.25
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0448   2263   0.926    887   0.834   3150   0.900  0.952  0.9645  0.9730  0.9044  0.9398
  0.1332   4414   0.872    883   0.765   5297   0.854  1.002  0.9470  0.9588  0.8960  0.9413
  0.2217   5844   0.888    887   0.777   6731   0.874  1.051  0.9584  0.9630  0.9162  0.9418
  0.3101   7026   0.828    892   0.756   7918   0.820  0.826  0.9187  0.9355  0.8544  0.9045
 $$
Resolution limits                    =     41.964     1.680
Number of used reflections           =      23096
Percentage observed                  =    99.9877
Percentage of free reflections       =     5.1070
Overall R factor                     =     0.1804
Free R factor                        =     0.2250
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9428
Overall weighted R factor            =     0.1607
Free weighted R factor               =     0.1996
Overall weighted R2 factor           =     0.1923
Free weighted R2 factor              =     0.2359
Average correlation coefficient      =     0.9286
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9334
Cruickshanks DPI for coordinate error=     0.1053
DPI based on free R factor           =     0.1084
Overall figure of merit              =     0.8544
ML based su of positional parameters =     0.0656
ML based su of thermal parameters    =     1.9647
-----------------------------------------------------------------------------
  Time in seconds: CPU =        18.96
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1804   0.2254   0.826      119212.    6583.0   0.0131  0.984   1.838  1.071   0.090
       1   0.1805   0.2247   0.852      118413.    6559.2   0.0121  0.908   1.781  1.036   0.087
       2   0.1801   0.2247   0.854      118284.    6556.3   0.0130  0.978   1.820  1.059   0.090
       3   0.1802   0.2249   0.854      118252.    6555.4   0.0132  0.988   1.834  1.068   0.091
       4   0.1802   0.2249   0.855      118242.    6555.2   0.0132  0.991   1.841  1.072   0.092
       5   0.1803   0.2249   0.855      118235.    6555.0   0.0132  0.993   1.844  1.073   0.092
       6   0.1803   0.2249   0.855      118234.    6555.0   0.0132  0.993   1.845  1.074   0.092
       7   0.1804   0.2249   0.854      118238.    6555.5   0.0132  0.994   1.846  1.075   0.092
       8   0.1804   0.2250   0.854      118242.    6555.7   0.0132  0.993   1.846  1.075   0.092
       9   0.1804   0.2250   0.854      118244.    6555.8   0.0132  0.993   1.846  1.075   0.092
      10   0.1804   0.2250   0.854      118242.    6555.7   0.0132  0.993   1.846  1.075   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1804   0.1804
             R free    0.2254   0.2250
     Rms BondLength    0.0131   0.0132
      Rms BondAngle    1.8379   1.8465
     Rms ChirVolume    0.0904   0.0918
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.1s System:    0.1s Elapsed:     0:51