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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: 13:03:43 


 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 1.98     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_1-99A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-98A.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_1-98A.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       0.0638
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9800
  Estimated number of reflections :      19530
  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  1.9800

  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_1-99A.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=   1.994 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=   2.204 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=   1.849 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=   2.220 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=   2.375 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=   2.445 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=   2.097 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        761
Number of   all  reflections      15047
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          15047

   Current auto weighting coefficient =    7.4496832    

 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.= 0.917 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        :   112  112  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    71   71  149
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    71   71  149
 Weight matrix   0.17819802    
 Actual weight    7.4496832      is applied to the X-ray term
Norm of X_ray positional gradient                28.7
Norm of Geom. positional gradient                77.4
Norm of X_ray B-factor gradient                  96.1
Norm of Geom. B-factor gradient                  97.6
Product of X_ray and Geom posit. gradients     -0.778E+07
 Cosine of angle between them                      -0.361
Product of X_ray and Geom B-fact gradients     -0.280E+08
 Cosine of angle between them                      -0.926


Residuals: XRAY=     0.5886E+06 GEOM=     0.1239E+05 TOTAL=     0.6010E+06
 function value    600970.13    

-------------------------------------------------------------------------------
             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     1.702     1.644
Bond angles  : others                          3238     2.341     1.580
Torsion angles, period  1. refined              185     7.181     5.000
Torsion angles, period  2. refined               90    36.145    22.778
Torsion angles, period  3. refined              268    14.676    15.000
Torsion angles, period  4. refined                9    12.113    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   303     0.244     0.200
VDW repulsions.others                          1346     0.220     0.200
VDW; torsion: refined_atoms                     712     0.169     0.200
VDW; torsion.others                             702     0.079     0.200
HBOND: refined_atoms                            237     0.205     0.200
HBOND.others                                      3     0.047     0.200
Metal-ion: refined_atoms                          1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 22     0.203     0.200
HBOND: symmetry: refined_atoms                   15     0.232     0.200
M. chain bond B values: refined atoms           746     1.465     1.189
M. chain bond B values: others                  746     1.464     1.189
M. chain angle B values: refined atoms          929     2.405     1.770
M. chain angle B values: others                 930     2.404     1.770
S. chain bond B values: refined atoms           811     2.332     1.500
S. chain bond B values: others                  810     2.327     1.500
S. chain angle B values: refined atoms         1177     3.727     2.112
S. chain angle B values: others                1178     3.725     2.111
Long range B values: refined atoms             1864     6.707    16.658
Long range B values: others                    1762     6.347    15.225
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1411
Partial structure    1: scale =     0.3743, B  =   48.3620
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    1975 100.00   483.4   485.8  0.16  0.17      91   474.6   484.1  0.20  0.22
 0.096    3299 100.00   416.1   397.4  0.16  0.15     165   414.9   384.0  0.22  0.21
 0.160    4151  99.95   261.0   259.4  0.16  0.14     243   276.9   271.6  0.23  0.20
 0.223    4853 100.00   213.9   211.5  0.16  0.13     262   213.8   215.2  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0324   1342   0.906    633   0.809   1975   0.874  0.963  0.9608  0.9686  0.9151  0.9421
  0.0960   2659   0.890    640   0.764   3299   0.865  1.000  0.9471  0.9632  0.8815  0.9444
  0.1596   3511   0.850    640   0.765   4151   0.837  0.963  0.9386  0.9535  0.8706  0.9398
  0.2233   4221   0.865    638   0.748   4859   0.850  0.966  0.9422  0.9571  0.8773  0.9410
 $$
Resolution limits                    =     41.964     1.980
Number of used reflections           =      14283
Percentage observed                  =    99.9801
Percentage of free reflections       =     5.0585
Overall R factor                     =     0.1578
Free R factor                        =     0.2201
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9443
Overall weighted R factor            =     0.1486
Free weighted R factor               =     0.2038
Overall weighted R2 factor           =     0.1810
Free weighted R2 factor              =     0.2428
Average correlation coefficient      =     0.9416
Overall correlation coefficient      =     0.9540
Free correlation coefficient         =     0.9072
Cruickshanks DPI for coordinate error=     0.1635
DPI based on free R factor           =     0.1590
Overall figure of merit              =     0.8531
ML based su of positional parameters =     0.0991
ML based su of thermal parameters    =     3.4257
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    79008.055       12385.105       600970.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.18614936    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595133.56    

-------------------------------------------------------------------------------
             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  =   -0.1513
Partial structure    1: scale =     0.3743, B  =   48.7784
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1578
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    78836.352       7827.7520       595133.56       600970.13    


     CGMAT cycle number =      3

 Weight matrix   0.18614596    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595155.69    

-------------------------------------------------------------------------------
             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  =   -0.1452
Partial structure    1: scale =     0.3738, B  =   48.9220
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1576
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9421
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02


 fvalues    78834.086       7867.6069       595181.44       595133.56    

 fvalues    78834.086       7867.6069       595164.31       595156.56    
 fvalues    78834.086       7867.6069       595164.31       595156.56    


     CGMAT cycle number =      4

 Weight matrix   0.18603154    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595169.94    

-------------------------------------------------------------------------------
             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  =   -0.1431
Partial structure    1: scale =     0.3739, B  =   48.9042
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1576
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9422
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02


 fvalues    78836.063       7865.4956       595172.63       595156.56    

 fvalues    78836.063       7865.4956       595162.44       595169.19    
 fvalues    78836.063       7865.4956       595162.44       595169.19    


     CGMAT cycle number =      5

 Weight matrix   0.18604408    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595163.25    

-------------------------------------------------------------------------------
             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  =   -0.1441
Partial structure    1: scale =     0.3739, B  =   48.8670
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1576
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9422
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    78835.672       7862.4873       595163.25       595169.19    


     CGMAT cycle number =      6

 Weight matrix   0.18579689    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595200.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1437
Partial structure    1: scale =     0.3738, B  =   48.8404
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1576
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9422
Overall figure of merit              =     0.8571
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    78838.438       7857.0317       595163.75       595163.25    
 fvalues    78838.438       7857.0317       595163.75       595178.44    


     CGMAT cycle number =      7

 Weight matrix   0.18603812    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595176.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1499
Partial structure    1: scale =     0.3739, B  =   48.9066
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1577
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9422
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    78839.078       7850.0146       595176.13       595178.44    


     CGMAT cycle number =      8

 Weight matrix   0.18580203    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595170.50    

-------------------------------------------------------------------------------
             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  =   -0.1506
Partial structure    1: scale =     0.3738, B  =   48.7758
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1577
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9422
Overall figure of merit              =     0.8571
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    78840.234       7835.7646       595170.50       595176.13    


     CGMAT cycle number =      9

 Weight matrix   0.18577552    
 Actual weight    7.4496832      is applied to the X-ray term


 function value    595181.25    

-------------------------------------------------------------------------------
             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  =   -0.1487
Partial structure    1: scale =     0.3739, B  =   48.7713
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1577
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9422
Overall figure of merit              =     0.8570
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    78842.063       7833.0146       595167.75       595170.50    
 fvalues    78842.063       7833.0146       595167.75       595181.38    


     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.= 0.930 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  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    71   71  149
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    71   71  149
 Weight matrix   0.18581419    
 Actual weight    7.4496832      is applied to the X-ray term
Norm of X_ray positional gradient                29.2
Norm of Geom. positional gradient                29.2
Norm of X_ray B-factor gradient                  96.3
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.822E+07
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.310E+08
 Cosine of angle between them                      -0.982


Residuals: XRAY=     0.5874E+06 GEOM=      7829.     TOTAL=     0.5952E+06
 function value    595184.69    

-------------------------------------------------------------------------------
             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     1.687     1.644
Bond angles  : others                          3238     1.401     1.580
Torsion angles, period  1. refined              185     7.154     5.000
Torsion angles, period  2. refined               90    36.160    22.778
Torsion angles, period  3. refined              268    14.603    15.000
Torsion angles, period  4. refined                9    11.804    15.000
Chiral centres: refined atoms                   196     0.081     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.243     0.200
VDW repulsions.others                          1352     0.196     0.200
VDW; torsion: refined_atoms                     712     0.169     0.200
VDW; torsion.others                             744     0.084     0.200
HBOND: refined_atoms                            230     0.209     0.200
HBOND.others                                      1     0.106     0.200
Metal-ion: refined_atoms                          1     0.008     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 23     0.179     0.200
HBOND: symmetry: refined_atoms                   16     0.222     0.200
HBOND: symmetry: others                           1     0.005     0.200
M. chain bond B values: refined atoms           746     1.466     1.190
M. chain bond B values: others                  746     1.465     1.190
M. chain angle B values: refined atoms          929     2.401     1.771
M. chain angle B values: others                 930     2.400     1.771
S. chain bond B values: refined atoms           811     2.321     1.499
S. chain bond B values: others                  810     2.317     1.499
S. chain angle B values: refined atoms         1177     3.705     2.111
S. chain angle B values: others                1178     3.704     2.111
Long range B values: refined atoms             1859     6.719    16.596
Long range B values: others                    1760     6.352    15.164
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1490
Partial structure    1: scale =     0.3739, B  =   48.8089
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    1975 100.00   484.4   486.7  0.16  0.17      91   475.6   485.6  0.20  0.22
 0.096    3299 100.00   416.9   397.8  0.16  0.15     165   415.8   383.4  0.22  0.21
 0.160    4151  99.95   261.5   259.8  0.16  0.14     243   277.5   272.0  0.23  0.20
 0.223    4853 100.00   214.3   212.0  0.15  0.12     262   214.3   216.3  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0324   1342   0.917    633   0.821   1975   0.886  0.963  0.9632  0.9708  0.9154  0.9420
  0.0960   2659   0.891    640   0.767   3299   0.867  1.000  0.9472  0.9634  0.8801  0.9436
  0.1596   3511   0.852    640   0.765   4151   0.838  0.963  0.9395  0.9542  0.8728  0.9401
  0.2233   4221   0.870    638   0.755   4859   0.855  0.966  0.9441  0.9591  0.8786  0.9430
 $$
Resolution limits                    =     41.964     1.980
Number of used reflections           =      14283
Percentage observed                  =    99.9801
Percentage of free reflections       =     5.0585
Overall R factor                     =     0.1577
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1487
Free weighted R factor               =     0.2036
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2432
Average correlation coefficient      =     0.9422
Overall correlation coefficient      =     0.9540
Free correlation coefficient         =     0.9072
Cruickshanks DPI for coordinate error=     0.1634
DPI based on free R factor           =     0.1588
Overall figure of merit              =     0.8571
ML based su of positional parameters =     0.0970
ML based su of thermal parameters    =     3.3543
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    78842.273       7828.9502       595178.88       595181.38    

    ****                              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.= 0.930 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_1-98A.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     1.687     1.644
Bond angles  : others                          3238     1.401     1.580
Torsion angles, period  1. refined              185     7.155     5.000
Torsion angles, period  2. refined               90    36.166    22.778
Torsion angles, period  3. refined              268    14.588    15.000
Torsion angles, period  4. refined                9    11.786    15.000
Chiral centres: refined atoms                   196     0.081     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.243     0.200
VDW repulsions.others                          1354     0.196     0.200
VDW; torsion: refined_atoms                     711     0.169     0.200
VDW; torsion.others                             754     0.083     0.200
HBOND: refined_atoms                            229     0.210     0.200
HBOND.others                                      1     0.107     0.200
Metal-ion: refined_atoms                          1     0.008     0.200
VDW repulsions: symmetry: refined_atoms           9     0.223     0.200
VDW repulsions: symmetry: others                 23     0.178     0.200
HBOND: symmetry: refined_atoms                   16     0.222     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           746     1.466     1.190
M. chain bond B values: others                  746     1.466     1.190
M. chain angle B values: refined atoms          929     2.402     1.771
M. chain angle B values: others                 930     2.401     1.771
S. chain bond B values: refined atoms           811     2.320     1.499
S. chain bond B values: others                  810     2.317     1.499
S. chain angle B values: refined atoms         1177     3.705     2.111
S. chain angle B values: others                1178     3.703     2.111
Long range B values: refined atoms             1857     6.686    16.554
Long range B values: others                    1759     6.316    15.151
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1452
Partial structure    1: scale =     0.3739, B  =   48.7165
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    1975 100.00   484.3   486.6  0.16  0.17      91   475.5   486.0  0.20  0.22
 0.096    3299 100.00   416.9   397.7  0.16  0.15     165   415.8   383.3  0.22  0.21
 0.160    4151  99.95   261.5   259.8  0.16  0.14     243   277.5   272.0  0.23  0.20
 0.223    4853 100.00   214.3   211.9  0.15  0.12     262   214.3   216.2  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0324   1342   0.917    633   0.821   1975   0.887  0.963  0.9633  0.9708  0.9154  0.9421
  0.0960   2659   0.891    640   0.767   3299   0.867  1.000  0.9472  0.9634  0.8801  0.9436
  0.1596   3511   0.852    640   0.764   4151   0.838  0.963  0.9396  0.9542  0.8729  0.9400
  0.2233   4221   0.870    638   0.755   4859   0.855  0.966  0.9441  0.9591  0.8785  0.9430
 $$
Resolution limits                    =     41.964     1.980
Number of used reflections           =      14283
Percentage observed                  =    99.9801
Percentage of free reflections       =     5.0585
Overall R factor                     =     0.1577
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1487
Free weighted R factor               =     0.2036
Overall weighted R2 factor           =     0.1814
Free weighted R2 factor              =     0.2431
Average correlation coefficient      =     0.9422
Overall correlation coefficient      =     0.9541
Free correlation coefficient         =     0.9073
Cruickshanks DPI for coordinate error=     0.1634
DPI based on free R factor           =     0.1587
Overall figure of merit              =     0.8571
ML based su of positional parameters =     0.0970
ML based su of thermal parameters    =     3.3543
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.61
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1578   0.2201   0.853       79008.    4366.9   0.0111  0.809   1.702  0.983   0.082
       1   0.1578   0.2196   0.857       78836.    4365.0   0.0107  0.781   1.674  0.968   0.081
       2   0.1576   0.2198   0.857       78834.    4365.8   0.0110  0.802   1.687  0.975   0.081
       3   0.1576   0.2198   0.857       78836.    4365.9   0.0110  0.802   1.687  0.976   0.081
       4   0.1576   0.2198   0.857       78836.    4365.9   0.0110  0.803   1.687  0.976   0.081
       5   0.1576   0.2198   0.857       78841.    4366.2   0.0110  0.803   1.687  0.976   0.081
       6   0.1577   0.2198   0.857       78839.    4366.0   0.0110  0.803   1.687  0.976   0.081
       7   0.1577   0.2198   0.857       78840.    4366.3   0.0110  0.803   1.687  0.976   0.081
       8   0.1577   0.2198   0.857       78842.    4366.4   0.0110  0.803   1.687  0.976   0.081
       9   0.1577   0.2198   0.857       78843.    4366.4   0.0110  0.803   1.687  0.976   0.081
      10   0.1577   0.2198   0.857       78840.    4366.3   0.0110  0.803   1.687  0.976   0.081
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1578   0.1577
             R free    0.2201   0.2198
     Rms BondLength    0.0111   0.0110
      Rms BondAngle    1.7023   1.6869
     Rms ChirVolume    0.0819   0.0808
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.6s System:    0.1s Elapsed:     0:49