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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: 10:40:40 


 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 1.70     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_step0-10A_R00_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-10A_R00_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-10A_R00_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  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  1.7000

  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_step0-10A_R00_1-80A.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=   2.048 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=   1.860 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=   2.209 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=   2.432 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=   2.412 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=   2.128 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       1202
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 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.= 0.920 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.27430516    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                38.0
Norm of Geom. positional gradient                78.9
Norm of X_ray B-factor gradient                  126.
Norm of Geom. B-factor gradient                  116.
Product of X_ray and Geom posit. gradients     -0.112E+08
 Cosine of angle between them                      -0.385
Product of X_ray and Geom B-fact gradients     -0.393E+08
 Cosine of angle between them                      -0.835


Residuals: XRAY=     0.7851E+06 GEOM=     0.1317E+05 TOTAL=     0.7983E+06
 function value    798303.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.794     1.644
Bond angles  : others                          3238     2.352     1.580
Torsion angles, period  1. refined              185     6.959     5.000
Torsion angles, period  2. refined               90    36.373    22.778
Torsion angles, period  3. refined              268    14.239    15.000
Torsion angles, period  4. refined                9    12.086    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   294     0.248     0.200
VDW repulsions.others                          1327     0.219     0.200
VDW; torsion: refined_atoms                     721     0.171     0.200
VDW; torsion.others                             721     0.081     0.200
HBOND: refined_atoms                            220     0.193     0.200
HBOND.others                                      1     0.009     0.200
VDW repulsions: symmetry: refined_atoms           8     0.214     0.200
VDW repulsions: symmetry: others                 21     0.203     0.200
HBOND: symmetry: refined_atoms                   21     0.199     0.200
M. chain bond B values: refined atoms           746     1.625     1.290
M. chain bond B values: others                  746     1.624     1.290
M. chain angle B values: refined atoms          929     2.561     1.920
M. chain angle B values: others                 930     2.560     1.920
S. chain bond B values: refined atoms           811     2.784     1.663
S. chain bond B values: others                  810     2.779     1.662
S. chain angle B values: refined atoms         1177     4.373     2.334
S. chain angle B values: others                1178     4.371     2.334
Long range B values: refined atoms             1841     6.831    17.819
Long range B values: others                    1749     6.501    16.399
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =    1.1269
Partial structure    1: scale =     0.3811, B  =   43.2245
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   454.8   463.5  0.16  0.17     135   453.2   460.9  0.21  0.22
 0.130    5109 100.00   299.3   286.3  0.16  0.15     291   305.4   282.4  0.22  0.20
 0.216    6518  99.97   202.5   186.2  0.17  0.15     354   208.0   193.2  0.20  0.17
 0.303    7621 100.00   104.5   117.1  0.26  0.20     422   102.5   114.9  0.32  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.909    857   0.812   3036   0.881  0.951  0.9602  0.9693  0.8998  0.9400
  0.1301   4247   0.868    862   0.762   5109   0.850  0.998  0.9450  0.9581  0.8944  0.9436
  0.2165   5641   0.879    877   0.769   6518   0.864  1.044  0.9523  0.9602  0.9064  0.9413
  0.3028   6772   0.757    852   0.688   7624   0.749  0.814  0.9038  0.9155  0.8508  0.8922
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1799
Free R factor                        =     0.2274
Average Fourier shell correlation    =     0.9457
AverageFree Fourier shell correlation=     0.9344
Overall weighted R factor            =     0.1592
Free weighted R factor               =     0.2019
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2379
Average correlation coefficient      =     0.9249
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9296
Cruickshanks DPI for coordinate error=     0.1091
DPI based on free R factor           =     0.1129
Overall figure of merit              =     0.8239
ML based su of positional parameters =     0.0760
ML based su of thermal parameters    =     2.3560
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116320.91       13173.412       798303.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33180523    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    787722.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0699
Partial structure    1: scale =     0.3813, B  =   43.2434
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1795
Free R factor                        =     0.2253
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9420
Average correlation coefficient      =     0.9263
Overall figure of merit              =     0.8501
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115504.65       8102.0459       787722.31       798303.19    


     CGMAT cycle number =      3

 Weight matrix   0.34288296    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786188.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0065
Partial structure    1: scale =     0.3815, B  =   42.9641
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1783
Free R factor                        =     0.2237
Average Fourier shell correlation    =     0.9539
AverageFree Fourier shell correlation=     0.9435
Average correlation coefficient      =     0.9284
Overall figure of merit              =     0.8532
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115187.01       8711.9678       786188.19       787722.31    


     CGMAT cycle number =      4

 Weight matrix   0.34809667    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785607.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0201
Partial structure    1: scale =     0.3817, B  =   42.8947
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2229
Average Fourier shell correlation    =     0.9544
AverageFree Fourier shell correlation=     0.9440
Average correlation coefficient      =     0.9290
Overall figure of merit              =     0.8545
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115064.66       8956.8467       785607.31       786188.19    


     CGMAT cycle number =      5

 Weight matrix   0.34941584    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785369.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0021
Partial structure    1: scale =     0.3820, B  =   42.8811
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2226
Average Fourier shell correlation    =     0.9545
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9294
Overall figure of merit              =     0.8548
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115014.70       9056.6436       785369.88       785607.31    


     CGMAT cycle number =      6

 Weight matrix   0.35044837    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785242.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0027
Partial structure    1: scale =     0.3821, B  =   42.8674
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.2226
Average Fourier shell correlation    =     0.9546
AverageFree Fourier shell correlation=     0.9444
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8551
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114986.60       9118.4189       785242.00       785369.88    


     CGMAT cycle number =      7

 Weight matrix   0.35052431    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785193.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0083
Partial structure    1: scale =     0.3826, B  =   42.9393
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.2225
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9444
Average correlation coefficient      =     0.9297
Overall figure of merit              =     0.8551
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114975.34       9145.5342       785193.19       785242.00    


     CGMAT cycle number =      8

 Weight matrix   0.35018766    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785112.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0214
Partial structure    1: scale =     0.3856, B  =   43.2837
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.2225
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9444
Average correlation coefficient      =     0.9297
Overall figure of merit              =     0.8551
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    114961.29       9159.2461       785112.00       785193.19    


     CGMAT cycle number =      9

 Weight matrix   0.35071450    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785070.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0041
Partial structure    1: scale =     0.3857, B  =   43.3185
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.2222
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9445
Average correlation coefficient      =     0.9297
Overall figure of merit              =     0.8552
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114955.73       9155.2354       785070.44       785112.00    


     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.= 0.914 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.35033780    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.7
Norm of Geom. positional gradient                41.6
Norm of X_ray B-factor gradient                  129.
Norm of Geom. B-factor gradient                  127.
Product of X_ray and Geom posit. gradients     -0.168E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.528E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7759E+06 GEOM=      9170.     TOTAL=     0.7851E+06
 function value    785066.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.830     1.644
Bond angles  : others                          3238     1.515     1.580
Torsion angles, period  1. refined              185     6.869     5.000
Torsion angles, period  2. refined               90    35.974    22.778
Torsion angles, period  3. refined              268    14.083    15.000
Torsion angles, period  4. refined                9    12.059    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.248     0.200
VDW repulsions.others                          1368     0.192     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             786     0.085     0.200
HBOND: refined_atoms                            210     0.192     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 21     0.181     0.200
HBOND: symmetry: refined_atoms                   20     0.195     0.200
M. chain bond B values: refined atoms           746     1.716     1.387
M. chain bond B values: others                  746     1.713     1.387
M. chain angle B values: refined atoms          929     2.687     2.068
M. chain angle B values: others                 930     2.685     2.068
S. chain bond B values: refined atoms           811     3.047     1.792
S. chain bond B values: others                  810     3.040     1.792
S. chain angle B values: refined atoms         1177     4.712     2.517
S. chain angle B values: others                1178     4.710     2.517
Long range B values: refined atoms             1832     7.043    19.235
Long range B values: others                    1742     6.771    17.790
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0129
Partial structure    1: scale =     0.3863, B  =   43.2150
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   454.2   463.3  0.16  0.17     135   452.6   462.2  0.20  0.21
 0.130    5109 100.00   298.9   285.4  0.16  0.15     291   305.0   282.9  0.21  0.19
 0.216    6518  99.97   202.2   186.1  0.17  0.15     354   207.7   192.6  0.20  0.17
 0.303    7621 100.00   104.4   116.3  0.25  0.19     422   102.4   115.1  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.926    857   0.835   3036   0.900  0.952  0.9648  0.9728  0.9020  0.9396
  0.1301   4247   0.873    862   0.767   5109   0.855  0.998  0.9480  0.9593  0.8998  0.9424
  0.2165   5641   0.890    877   0.782   6518   0.875  1.044  0.9572  0.9633  0.9139  0.9417
  0.3028   6772   0.828    852   0.751   7624   0.820  0.840  0.9248  0.9370  0.8614  0.9071
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1777
Free R factor                        =     0.2224
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1590
Free weighted R factor               =     0.1967
Overall weighted R2 factor           =     0.1910
Free weighted R2 factor              =     0.2315
Average correlation coefficient      =     0.9297
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9327
Cruickshanks DPI for coordinate error=     0.1078
DPI based on free R factor           =     0.1105
Overall figure of merit              =     0.8551
ML based su of positional parameters =     0.0672
ML based su of thermal parameters    =     2.0343
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114953.01       9169.9688       785066.88       785070.44    

    ****                              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.= 0.914 id.= 3.000 dev= -2.09 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_step0-10A_R00_1-70A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.830     1.644
Bond angles  : others                          3238     1.515     1.580
Torsion angles, period  1. refined              185     6.867     5.000
Torsion angles, period  2. refined               90    35.939    22.778
Torsion angles, period  3. refined              268    14.088    15.000
Torsion angles, period  4. refined                9    12.051    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.248     0.200
VDW repulsions.others                          1369     0.192     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             789     0.085     0.200
HBOND: refined_atoms                            210     0.192     0.200
HBOND.others                                      1     0.010     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 22     0.178     0.200
HBOND: symmetry: refined_atoms                   21     0.190     0.200
M. chain bond B values: refined atoms           746     1.715     1.386
M. chain bond B values: others                  746     1.712     1.386
M. chain angle B values: refined atoms          929     2.684     2.067
M. chain angle B values: others                 930     2.683     2.067
S. chain bond B values: refined atoms           811     3.048     1.792
S. chain bond B values: others                  810     3.040     1.792
S. chain angle B values: refined atoms         1177     4.712     2.517
S. chain angle B values: others                1178     4.710     2.516
Long range B values: refined atoms             1833     7.047    19.220
Long range B values: others                    1744     6.775    17.803
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0112
Partial structure    1: scale =     0.3864, B  =   43.1931
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   454.2   463.2  0.16  0.17     135   452.6   462.2  0.20  0.21
 0.130    5109 100.00   298.9   285.5  0.16  0.15     291   305.0   283.0  0.21  0.19
 0.216    6518  99.97   202.2   186.1  0.17  0.14     354   207.7   192.5  0.20  0.17
 0.303    7621 100.00   104.4   116.3  0.25  0.19     422   102.3   115.1  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.926    857   0.835   3036   0.900  0.952  0.9647  0.9728  0.9018  0.9395
  0.1301   4247   0.873    862   0.767   5109   0.855  0.998  0.9480  0.9593  0.8999  0.9424
  0.2165   5641   0.890    877   0.782   6518   0.875  1.044  0.9573  0.9634  0.9141  0.9417
  0.3028   6772   0.828    852   0.751   7624   0.820  0.840  0.9248  0.9370  0.8613  0.9072
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1777
Free R factor                        =     0.2224
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1590
Free weighted R factor               =     0.1967
Overall weighted R2 factor           =     0.1910
Free weighted R2 factor              =     0.2317
Average correlation coefficient      =     0.9297
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9327
Cruickshanks DPI for coordinate error=     0.1078
DPI based on free R factor           =     0.1105
Overall figure of merit              =     0.8551
ML based su of positional parameters =     0.0672
ML based su of thermal parameters    =     2.0343
-----------------------------------------------------------------------------
  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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1799   0.2274   0.824      116321.    6439.5   0.0121  0.903   1.794  1.031   0.084
       1   0.1795   0.2253   0.850      115505.    6409.4   0.0117  0.877   1.758  1.011   0.084
       2   0.1783   0.2237   0.853      115187.    6397.0   0.0126  0.946   1.792  1.034   0.087
       3   0.1781   0.2229   0.854      115065.    6391.5   0.0128  0.960   1.808  1.045   0.089
       4   0.1779   0.2226   0.855      115015.    6389.2   0.0128  0.966   1.818  1.052   0.090
       5   0.1778   0.2226   0.855      114987.    6388.0   0.0129  0.968   1.823  1.055   0.090
       6   0.1778   0.2225   0.855      114975.    6387.4   0.0129  0.969   1.826  1.057   0.090
       7   0.1778   0.2225   0.855      114961.    6386.8   0.0129  0.968   1.827  1.059   0.090
       8   0.1778   0.2222   0.855      114956.    6386.6   0.0129  0.968   1.828  1.059   0.090
       9   0.1777   0.2224   0.855      114953.    6386.6   0.0129  0.969   1.830  1.060   0.090
      10   0.1777   0.2224   0.855      114951.    6386.7   0.0129  0.969   1.830  1.061   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1799   0.1777
             R free    0.2274   0.2224
     Rms BondLength    0.0121   0.0129
      Rms BondAngle    1.7944   1.8301
     Rms ChirVolume    0.0844   0.0905
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.5s System:    0.1s Elapsed:     0:46