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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 13:10:31 


 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 1.96     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_1-97A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-96A.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_1-96A.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       0.0651
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9600
  Estimated number of reflections :      19845
  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  1.9600

  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_1-97A.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=   1.982 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=   2.211 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=   1.847 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=   2.211 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=   2.355 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=   2.439 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=   2.089 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        783
Number of   all  reflections      15506
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          15506

   Current auto weighting coefficient =    7.3995371    

 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.= 0.915 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Weight matrix   0.19023827    
 Actual weight    7.3995371      is applied to the X-ray term
Norm of X_ray positional gradient                30.1
Norm of Geom. positional gradient                77.0
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  99.2
Product of X_ray and Geom posit. gradients     -0.805E+07
 Cosine of angle between them                      -0.358
Product of X_ray and Geom B-fact gradients     -0.305E+08
 Cosine of angle between them                      -0.926


Residuals: XRAY=     0.6008E+06 GEOM=     0.1229E+05 TOTAL=     0.6131E+06
 function value    613071.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.678     1.644
Bond angles  : others                          3238     2.333     1.580
Torsion angles, period  1. refined              185     7.083     5.000
Torsion angles, period  2. refined               90    36.503    22.778
Torsion angles, period  3. refined              268    14.435    15.000
Torsion angles, period  4. refined                9    11.473    15.000
Chiral centres: refined atoms                   196     0.080     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   304     0.241     0.200
VDW repulsions.others                          1330     0.219     0.200
VDW; torsion: refined_atoms                     711     0.169     0.200
VDW; torsion.others                             711     0.079     0.200
HBOND: refined_atoms                            234     0.209     0.200
HBOND.others                                      1     0.062     0.200
Metal-ion: refined_atoms                          1     0.018     0.200
VDW repulsions: symmetry: refined_atoms           9     0.229     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   18     0.227     0.200
M. chain bond B values: refined atoms           746     1.480     1.189
M. chain bond B values: others                  746     1.480     1.190
M. chain angle B values: refined atoms          929     2.419     1.770
M. chain angle B values: others                 930     2.417     1.770
S. chain bond B values: refined atoms           811     2.310     1.498
S. chain bond B values: others                  810     2.307     1.498
S. chain angle B values: refined atoms         1177     3.694     2.110
S. chain angle B values: others                1178     3.692     2.109
Long range B values: refined atoms             1862     6.706    16.634
Long range B values: others                    1760     6.312    15.181
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1137
Partial structure    1: scale =     0.3735, B  =   46.3087
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2031 100.00   484.8   487.0  0.16  0.17      91   475.0   486.8  0.20  0.22
 0.098    3400 100.00   410.1   391.9  0.16  0.15     172   406.8   376.0  0.23  0.21
 0.163    4261  99.96   257.7   255.5  0.16  0.14     253   274.5   266.7  0.22  0.19
 0.228    5024 100.00   209.2   207.3  0.16  0.13     267   212.6   215.7  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0330   1386   0.909    645   0.814   2031   0.879  0.964  0.9616  0.9693  0.9158  0.9434
  0.0980   2748   0.885    652   0.766   3400   0.862  0.998  0.9444  0.9616  0.8800  0.9428
  0.1629   3609   0.851    652   0.762   4261   0.838  0.965  0.9402  0.9539  0.8778  0.9394
  0.2278   4374   0.868    655   0.748   5029   0.852  0.965  0.9449  0.9578  0.8781  0.9409
 $$
Resolution limits                    =     41.964     1.960
Number of used reflections           =      14721
Percentage observed                  =    99.9807
Percentage of free reflections       =     5.0503
Overall R factor                     =     0.1586
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9452
Overall weighted R factor            =     0.1492
Free weighted R factor               =     0.2027
Overall weighted R2 factor           =     0.1812
Free weighted R2 factor              =     0.2441
Average correlation coefficient      =     0.9413
Overall correlation coefficient      =     0.9543
Free correlation coefficient         =     0.9079
Cruickshanks DPI for coordinate error=     0.1578
DPI based on free R factor           =     0.1536
Overall figure of merit              =     0.8540
ML based su of positional parameters =     0.0956
ML based su of thermal parameters    =     3.2583
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    81192.141       12287.594       613071.88      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.19762799    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607347.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1380
Partial structure    1: scale =     0.3736, B  =   46.5496
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9417
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    81015.195       7872.4282       607347.38       613071.88    


     CGMAT cycle number =      3

 Weight matrix   0.19783768    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607277.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1221
Partial structure    1: scale =     0.3737, B  =   46.5204
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    80997.703       7931.5713       607277.06       607347.38    


     CGMAT cycle number =      4

 Weight matrix   0.19784005    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607253.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1242
Partial structure    1: scale =     0.3738, B  =   46.4199
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    80993.203       7940.8135       607253.00       607277.06    


     CGMAT cycle number =      5

 Weight matrix   0.19782674    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607233.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1309
Partial structure    1: scale =     0.3738, B  =   46.3898
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    80990.766       7938.8467       607233.06       607253.00    


     CGMAT cycle number =      6

 Weight matrix   0.19774663    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607209.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1339
Partial structure    1: scale =     0.3739, B  =   46.3436
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    80988.250       7933.7881       607209.38       607233.06    


     CGMAT cycle number =      7

 Weight matrix   0.19761151    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607199.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1363
Partial structure    1: scale =     0.3741, B  =   46.1793
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    80988.047       7925.2676       607199.31       607209.38    


     CGMAT cycle number =      8

 Weight matrix   0.19721627    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607228.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1444
Partial structure    1: scale =     0.3742, B  =   46.0959
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2177
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    80993.219       7916.1250       607229.00       607199.31    

 fvalues    80993.219       7916.1250       607229.31       607228.44    
 fvalues    80993.219       7916.1250       607229.31       607228.44    


     CGMAT cycle number =      9

 Weight matrix   0.19697733    
 Actual weight    7.3995371      is applied to the X-ray term


 function value    607259.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1381
Partial structure    1: scale =     0.3741, B  =   46.0606
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2177
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    80998.172       7913.6016       607244.75       607228.44    
 fvalues    80998.172       7913.6016       607244.75       607262.63    


     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.= 0.931 id.= 3.000 dev= -2.07 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        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Weight matrix   0.19706370    
 Actual weight    7.3995371      is applied to the X-ray term
Norm of X_ray positional gradient                30.1
Norm of Geom. positional gradient                30.1
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.875E+07
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.340E+08
 Cosine of angle between them                      -0.984


Residuals: XRAY=     0.5993E+06 GEOM=      7911.     TOTAL=     0.6072E+06
 function value    607247.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.680     1.644
Bond angles  : others                          3238     1.405     1.580
Torsion angles, period  1. refined              185     7.113     5.000
Torsion angles, period  2. refined               90    36.640    22.778
Torsion angles, period  3. refined              268    14.473    15.000
Torsion angles, period  4. refined                9    11.230    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.241     0.200
VDW repulsions.others                          1366     0.191     0.200
VDW; torsion: refined_atoms                     706     0.170     0.200
VDW; torsion.others                             781     0.082     0.200
HBOND: refined_atoms                            238     0.207     0.200
HBOND.others                                      1     0.009     0.200
Metal-ion: refined_atoms                          1     0.018     0.200
VDW repulsions: symmetry: refined_atoms           8     0.243     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   17     0.237     0.200
HBOND: symmetry: others                           1     0.005     0.200
M. chain bond B values: refined atoms           746     1.497     1.190
M. chain bond B values: others                  746     1.496     1.190
M. chain angle B values: refined atoms          929     2.435     1.770
M. chain angle B values: others                 930     2.434     1.770
S. chain bond B values: refined atoms           811     2.335     1.502
S. chain bond B values: others                  810     2.332     1.502
S. chain angle B values: refined atoms         1177     3.728     2.114
S. chain angle B values: others                1178     3.726     2.114
Long range B values: refined atoms             1860     6.703    16.637
Long range B values: others                    1760     6.342    15.201
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1363
Partial structure    1: scale =     0.3742, B  =   46.0420
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2031 100.00   485.5   487.5  0.16  0.17      91   475.6   487.4  0.20  0.22
 0.098    3400 100.00   410.7   392.0  0.16  0.15     172   407.3   376.7  0.22  0.21
 0.163    4261  99.96   258.1   255.9  0.16  0.14     253   274.9   266.6  0.22  0.19
 0.228    5024 100.00   209.5   207.6  0.15  0.12     267   212.9   215.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0330   1386   0.919    645   0.823   2031   0.888  0.964  0.9632  0.9711  0.9135  0.9433
  0.0980   2748   0.889    652   0.770   3400   0.867  0.998  0.9464  0.9631  0.8820  0.9432
  0.1629   3609   0.852    652   0.762   4261   0.838  0.965  0.9405  0.9539  0.8790  0.9387
  0.2278   4374   0.871    655   0.751   5029   0.856  0.965  0.9465  0.9595  0.8807  0.9432
 $$
Resolution limits                    =     41.964     1.960
Number of used reflections           =      14721
Percentage observed                  =    99.9807
Percentage of free reflections       =     5.0503
Overall R factor                     =     0.1581
Free R factor                        =     0.2177
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Overall weighted R factor            =     0.1491
Free weighted R factor               =     0.2028
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2444
Average correlation coefficient      =     0.9419
Overall correlation coefficient      =     0.9545
Free correlation coefficient         =     0.9085
Cruickshanks DPI for coordinate error=     0.1573
DPI based on free R factor           =     0.1533
Overall figure of merit              =     0.8576
ML based su of positional parameters =     0.0938
ML based su of thermal parameters    =     3.2049
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    80996.492       7910.5542       607247.13       607262.63    

    ****                              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.= 0.931 id.= 3.000 dev= -2.07 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_1-96A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.680     1.644
Bond angles  : others                          3238     1.405     1.580
Torsion angles, period  1. refined              185     7.112     5.000
Torsion angles, period  2. refined               90    36.634    22.778
Torsion angles, period  3. refined              268    14.477    15.000
Torsion angles, period  4. refined                9    11.225    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.241     0.200
VDW repulsions.others                          1368     0.191     0.200
VDW; torsion: refined_atoms                     707     0.170     0.200
VDW; torsion.others                             782     0.082     0.200
HBOND: refined_atoms                            238     0.207     0.200
HBOND.others                                      1     0.008     0.200
Metal-ion: refined_atoms                          1     0.018     0.200
VDW repulsions: symmetry: refined_atoms           8     0.244     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   17     0.237     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           746     1.496     1.189
M. chain bond B values: others                  746     1.495     1.190
M. chain angle B values: refined atoms          929     2.435     1.770
M. chain angle B values: others                 930     2.434     1.770
S. chain bond B values: refined atoms           811     2.334     1.502
S. chain bond B values: others                  810     2.331     1.501
S. chain angle B values: refined atoms         1177     3.726     2.114
S. chain angle B values: others                1178     3.725     2.113
Long range B values: refined atoms             1860     6.702    16.647
Long range B values: others                    1760     6.341    15.212
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1356
Partial structure    1: scale =     0.3742, B  =   46.0349
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2031 100.00   485.4   487.5  0.16  0.17      91   475.6   487.3  0.20  0.22
 0.098    3400 100.00   410.6   392.0  0.16  0.15     172   407.3   376.7  0.22  0.21
 0.163    4261  99.96   258.0   255.9  0.16  0.14     253   274.9   266.6  0.22  0.19
 0.228    5024 100.00   209.5   207.6  0.15  0.12     267   212.9   215.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0330   1386   0.919    645   0.823   2031   0.888  0.964  0.9632  0.9711  0.9135  0.9433
  0.0980   2748   0.890    652   0.770   3400   0.867  0.998  0.9464  0.9631  0.8819  0.9432
  0.1629   3609   0.852    652   0.762   4261   0.838  0.965  0.9405  0.9539  0.8789  0.9387
  0.2278   4374   0.871    655   0.751   5029   0.856  0.965  0.9465  0.9595  0.8807  0.9432
 $$
Resolution limits                    =     41.964     1.960
Number of used reflections           =      14721
Percentage observed                  =    99.9807
Percentage of free reflections       =     5.0503
Overall R factor                     =     0.1581
Free R factor                        =     0.2177
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Overall weighted R factor            =     0.1491
Free weighted R factor               =     0.2028
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2444
Average correlation coefficient      =     0.9419
Overall correlation coefficient      =     0.9545
Free correlation coefficient         =     0.9085
Cruickshanks DPI for coordinate error=     0.1573
DPI based on free R factor           =     0.1533
Overall figure of merit              =     0.8576
ML based su of positional parameters =     0.0938
ML based su of thermal parameters    =     3.2049
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.96
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1586   0.2181   0.854       81192.    4480.7   0.0110  0.806   1.678  0.974   0.080
       1   0.1585   0.2174   0.858       81015.    4477.6   0.0108  0.790   1.660  0.964   0.081
       2   0.1582   0.2174   0.858       80998.    4477.3   0.0111  0.811   1.674  0.973   0.081
       3   0.1581   0.2175   0.858       80993.    4477.3   0.0111  0.812   1.678  0.975   0.082
       4   0.1581   0.2175   0.858       80991.    4477.3   0.0111  0.812   1.679  0.976   0.082
       5   0.1581   0.2175   0.858       80988.    4477.2   0.0111  0.813   1.680  0.977   0.082
       6   0.1581   0.2175   0.858       80988.    4477.3   0.0111  0.813   1.680  0.978   0.082
       7   0.1581   0.2177   0.858       80993.    4477.8   0.0111  0.812   1.680  0.978   0.082
       8   0.1581   0.2177   0.858       80998.    4478.0   0.0111  0.812   1.680  0.978   0.082
       9   0.1581   0.2177   0.858       80996.    4477.9   0.0111  0.812   1.680  0.978   0.082
      10   0.1581   0.2177   0.858       80995.    4477.8   0.0111  0.812   1.680  0.978   0.082
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1586   0.1581
             R free    0.2181   0.2177
     Rms BondLength    0.0110   0.0111
      Rms BondAngle    1.6777   1.6803
     Rms ChirVolume    0.0803   0.0816
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.0s System:    0.1s Elapsed:     0:46