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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: 14:08:35 


 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 1.87     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_1-88A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-87A.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_1-87A.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       0.0715
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8700
  Estimated number of reflections :      22199
  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  1.8700

  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_1-88A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.017 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=   2.212 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=   1.880 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=   2.236 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=   2.394 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=   2.430 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=   2.136 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        906
Number of   all  reflections      17789
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          17789

   Current auto weighting coefficient =    7.1746697    

 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.= 0.943 id.= 3.000 dev= -2.06 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                 :    31   31   66
 Minimum acceptable grid spacing:    74   74  156
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   66
 Minimum acceptable grid spacing:    74   74  156
 Weight matrix   0.22693099    
 Actual weight    7.1746697      is applied to the X-ray term
Norm of X_ray positional gradient                31.7
Norm of Geom. positional gradient                77.9
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.944E+07
 Cosine of angle between them                      -0.395
Product of X_ray and Geom B-fact gradients     -0.353E+08
 Cosine of angle between them                      -0.942


Residuals: XRAY=     0.6567E+06 GEOM=     0.1276E+05 TOTAL=     0.6695E+06
 function value    669479.56    

-------------------------------------------------------------------------------
             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     1.734     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     6.971     5.000
Torsion angles, period  2. refined               90    36.500    22.778
Torsion angles, period  3. refined              268    13.579    15.000
Torsion angles, period  4. refined                9    11.159    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   300     0.241     0.200
VDW repulsions.others                          1345     0.218     0.200
VDW; torsion: refined_atoms                     716     0.171     0.200
VDW; torsion.others                             716     0.079     0.200
HBOND: refined_atoms                            227     0.209     0.200
VDW repulsions: symmetry: refined_atoms           7     0.240     0.200
VDW repulsions: symmetry: others                 24     0.202     0.200
HBOND: symmetry: refined_atoms                   21     0.208     0.200
M. chain bond B values: refined atoms           746     1.561     1.233
M. chain bond B values: others                  746     1.560     1.233
M. chain angle B values: refined atoms          929     2.508     1.835
M. chain angle B values: others                 930     2.507     1.834
S. chain bond B values: refined atoms           812     2.524     1.571
S. chain bond B values: others                  811     2.522     1.570
S. chain angle B values: refined atoms         1177     3.965     2.210
S. chain angle B values: others                1178     3.963     2.209
Long range B values: refined atoms             1855     6.609    17.042
Long range B values: others                    1761     6.335    15.723
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0405, B  =   -0.0035
Partial structure    1: scale =     0.3761, B  =   46.6099
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.036    2322 100.00   478.6   484.2  0.16  0.17     104   472.8   481.9  0.20  0.22
 0.108    3890 100.00   373.1   356.5  0.16  0.15     204   378.0   352.1  0.21  0.20
 0.179    4906  99.96   241.7   234.8  0.16  0.13     289   251.4   239.2  0.22  0.19
 0.250    5754 100.00   176.3   178.4  0.17  0.14     309   180.0   183.1  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0362   1612   0.914    710   0.808   2322   0.881  0.959  0.9615  0.9690  0.9099  0.9406
  0.1076   3172   0.880    718   0.773   3890   0.860  0.995  0.9472  0.9619  0.8851  0.9447
  0.1789   4193   0.869    713   0.765   4906   0.854  0.989  0.9444  0.9577  0.8848  0.9388
  0.2503   5044   0.848    719   0.735   5763   0.834  0.937  0.9381  0.9517  0.8683  0.9340
 $$
Resolution limits                    =     41.964     1.870
Number of used reflections           =      16881
Percentage observed                  =    99.9831
Percentage of free reflections       =     5.0936
Overall R factor                     =     0.1623
Free R factor                        =     0.2162
Average Fourier shell correlation    =     0.9582
AverageFree Fourier shell correlation=     0.9448
Overall weighted R factor            =     0.1508
Free weighted R factor               =     0.1997
Overall weighted R2 factor           =     0.1837
Free weighted R2 factor              =     0.2409
Average correlation coefficient      =     0.9388
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9153
Cruickshanks DPI for coordinate error=     0.1355
DPI based on free R factor           =     0.1357
Overall figure of merit              =     0.8524
ML based su of positional parameters =     0.0862
ML based su of thermal parameters    =     2.8397
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    91533.664       12755.752       669479.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.23779759    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663386.69    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0956
Partial structure    1: scale =     0.3763, B  =   46.6778
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2154
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9390
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    91320.711       8190.7363       663386.69       669479.56    


     CGMAT cycle number =      3

 Weight matrix   0.23824206    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663275.06    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0816
Partial structure    1: scale =     0.3763, B  =   46.5783
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1621
Free R factor                        =     0.2152
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9392
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    91294.164       8269.5898       663275.06       663386.69    


     CGMAT cycle number =      4

 Weight matrix   0.23847964    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663239.38    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0831
Partial structure    1: scale =     0.3762, B  =   46.7305
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1620
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    91287.000       8285.2832       663239.38       663275.06    


     CGMAT cycle number =      5

 Weight matrix   0.23863630    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663172.00    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0782
Partial structure    1: scale =     0.3765, B  =   46.6664
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1619
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    91276.789       8291.1582       663172.00       663239.38    


     CGMAT cycle number =      6

 Weight matrix   0.23867756    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663152.13    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0855
Partial structure    1: scale =     0.3766, B  =   46.4787
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1619
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    91274.758       8285.8975       663152.13       663172.00    


     CGMAT cycle number =      7

 Weight matrix   0.23876731    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663120.38    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0838
Partial structure    1: scale =     0.3767, B  =   46.4309
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1619
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8580
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    91270.758       8282.7842       663120.38       663152.13    


     CGMAT cycle number =      8

 Weight matrix   0.23855282    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663136.38    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0856
Partial structure    1: scale =     0.3767, B  =   46.4525
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1619
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    91272.984       8282.7031       663104.69       663120.38    
 fvalues    91272.984       8282.7031       663104.69       663136.19    


     CGMAT cycle number =      9

 Weight matrix   0.23868686    
 Actual weight    7.1746697      is applied to the X-ray term


 function value    663107.06    

-------------------------------------------------------------------------------
             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 =     0.0405, B  =   -0.0800
Partial structure    1: scale =     0.3769, B  =   46.5307
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1619
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8580
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    91270.305       8272.7422       663107.06       663136.19    


     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.= 0.946 id.= 3.000 dev= -2.05 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                 :    31   31   66
 Minimum acceptable grid spacing:    74   74  156
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   66
 Minimum acceptable grid spacing:    74   74  156
 Weight matrix   0.23864122    
 Actual weight    7.1746697      is applied to the X-ray term
Norm of X_ray positional gradient                32.5
Norm of Geom. positional gradient                32.5
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.102E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.393E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.6548E+06 GEOM=      8271.     TOTAL=     0.6631E+06
 function value    663107.50    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.736     1.644
Bond angles  : others                          3238     1.443     1.580
Torsion angles, period  1. refined              185     6.971     5.000
Torsion angles, period  2. refined               90    36.173    22.778
Torsion angles, period  3. refined              268    13.479    15.000
Torsion angles, period  4. refined                9    11.222    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.243     0.200
VDW repulsions.others                          1375     0.189     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             790     0.083     0.200
HBOND: refined_atoms                            224     0.211     0.200
VDW repulsions: symmetry: refined_atoms           8     0.230     0.200
VDW repulsions: symmetry: others                 24     0.197     0.200
HBOND: symmetry: refined_atoms                   20     0.206     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           746     1.565     1.241
M. chain bond B values: others                  746     1.564     1.241
M. chain angle B values: refined atoms          929     2.511     1.848
M. chain angle B values: others                 930     2.509     1.847
S. chain bond B values: refined atoms           811     2.540     1.582
S. chain bond B values: others                  810     2.538     1.581
S. chain angle B values: refined atoms         1177     3.986     2.225
S. chain angle B values: others                1178     3.984     2.224
Long range B values: refined atoms             1851     6.654    17.148
Long range B values: others                    1756     6.341    15.782
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0405, B  =   -0.0821
Partial structure    1: scale =     0.3768, B  =   46.5871
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.036    2322 100.00   478.8   484.5  0.16  0.17     104   473.1   482.4  0.20  0.22
 0.108    3890 100.00   373.3   356.6  0.16  0.15     204   378.2   352.1  0.21  0.19
 0.179    4906  99.96   241.9   234.9  0.16  0.13     289   251.5   239.1  0.22  0.19
 0.250    5754 100.00   176.4   178.6  0.17  0.13     309   180.1   183.4  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0362   1612   0.924    710   0.822   2322   0.893  0.959  0.9645  0.9715  0.9113  0.9411
  0.1076   3172   0.883    718   0.778   3890   0.864  0.995  0.9486  0.9629  0.8866  0.9444
  0.1789   4193   0.871    713   0.767   4906   0.856  0.989  0.9449  0.9581  0.8857  0.9390
  0.2503   5044   0.856    719   0.743   5763   0.842  0.937  0.9409  0.9540  0.8718  0.9354
 $$
Resolution limits                    =     41.964     1.870
Number of used reflections           =      16881
Percentage observed                  =    99.9831
Percentage of free reflections       =     5.0936
Overall R factor                     =     0.1619
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1506
Free weighted R factor               =     0.1981
Overall weighted R2 factor           =     0.1835
Free weighted R2 factor              =     0.2387
Average correlation coefficient      =     0.9393
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9165
Cruickshanks DPI for coordinate error=     0.1352
DPI based on free R factor           =     0.1349
Overall figure of merit              =     0.8580
ML based su of positional parameters =     0.0840
ML based su of thermal parameters    =     2.7649
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    91270.734       8271.3564       663096.13       663107.06    
 fvalues    91270.734       8271.3564       663096.13       663108.75    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.946 id.= 3.000 dev= -2.05 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_1-87A.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     1.736     1.644
Bond angles  : others                          3238     1.443     1.580
Torsion angles, period  1. refined              185     6.970     5.000
Torsion angles, period  2. refined               90    36.150    22.778
Torsion angles, period  3. refined              268    13.471    15.000
Torsion angles, period  4. refined                9    11.241    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.243     0.200
VDW repulsions.others                          1376     0.189     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             792     0.083     0.200
HBOND: refined_atoms                            224     0.211     0.200
VDW repulsions: symmetry: refined_atoms           8     0.231     0.200
VDW repulsions: symmetry: others                 25     0.193     0.200
HBOND: symmetry: refined_atoms                   20     0.206     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           746     1.565     1.241
M. chain bond B values: others                  746     1.564     1.241
M. chain angle B values: refined atoms          929     2.511     1.848
M. chain angle B values: others                 930     2.510     1.847
S. chain bond B values: refined atoms           811     2.540     1.582
S. chain bond B values: others                  810     2.538     1.582
S. chain angle B values: refined atoms         1177     3.987     2.225
S. chain angle B values: others                1178     3.985     2.224
Long range B values: refined atoms             1852     6.654    17.148
Long range B values: others                    1757     6.341    15.782
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0405, B  =   -0.0814
Partial structure    1: scale =     0.3767, B  =   46.5306
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.036    2322 100.00   478.8   484.5  0.16  0.17     104   473.0   482.4  0.20  0.22
 0.108    3890 100.00   373.2   356.6  0.16  0.15     204   378.2   352.1  0.21  0.19
 0.179    4906  99.96   241.8   234.9  0.16  0.13     289   251.5   239.1  0.22  0.19
 0.250    5754 100.00   176.4   178.6  0.17  0.13     309   180.1   183.4  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0362   1612   0.924    710   0.822   2322   0.893  0.959  0.9645  0.9716  0.9115  0.9412
  0.1076   3172   0.883    718   0.778   3890   0.864  0.995  0.9485  0.9629  0.8864  0.9444
  0.1789   4193   0.871    713   0.767   4906   0.856  0.989  0.9449  0.9581  0.8857  0.9389
  0.2503   5044   0.856    719   0.743   5763   0.842  0.937  0.9409  0.9541  0.8718  0.9354
 $$
Resolution limits                    =     41.964     1.870
Number of used reflections           =      16881
Percentage observed                  =    99.9831
Percentage of free reflections       =     5.0936
Overall R factor                     =     0.1619
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1506
Free weighted R factor               =     0.1980
Overall weighted R2 factor           =     0.1835
Free weighted R2 factor              =     0.2386
Average correlation coefficient      =     0.9393
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9165
Cruickshanks DPI for coordinate error=     0.1352
DPI based on free R factor           =     0.1349
Overall figure of merit              =     0.8580
ML based su of positional parameters =     0.0840
ML based su of thermal parameters    =     2.7649
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.37
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1623   0.2162   0.852       91534.    5085.9   0.0114  0.847   1.734  1.007   0.084
       1   0.1624   0.2154   0.857       91321.    5081.8   0.0111  0.824   1.711  0.994   0.084
       2   0.1621   0.2152   0.858       91294.    5081.1   0.0114  0.848   1.725  1.002   0.084
       3   0.1620   0.2151   0.858       91287.    5080.7   0.0115  0.851   1.729  1.004   0.084
       4   0.1619   0.2150   0.858       91277.    5080.0   0.0115  0.852   1.731  1.005   0.084
       5   0.1619   0.2149   0.858       91275.    5079.8   0.0115  0.853   1.732  1.006   0.084
       6   0.1619   0.2149   0.858       91271.    5079.6   0.0115  0.853   1.733  1.006   0.084
       7   0.1619   0.2149   0.858       91273.    5079.9   0.0115  0.853   1.735  1.007   0.084
       8   0.1619   0.2149   0.858       91270.    5079.7   0.0115  0.853   1.735  1.007   0.084
       9   0.1619   0.2149   0.858       91271.    5079.6   0.0115  0.854   1.736  1.008   0.084
      10   0.1619   0.2149   0.858       91267.    5079.5   0.0115  0.854   1.736  1.008   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1623   0.1619
             R free    0.2162   0.2149
     Rms BondLength    0.0114   0.0115
      Rms BondAngle    1.7345   1.7361
     Rms ChirVolume    0.0839   0.0840
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.4s System:    0.1s Elapsed:     0:47