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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: 15:20:21 


 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 1.80     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 4
  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_complete_R04_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R04_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R04_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:     4
  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  1.8000

  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_complete_R04_1-90A.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=   2.020 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=   2.196 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=   1.842 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=   2.203 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=   2.366 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=   2.420 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=   2.085 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:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            4
Number of "free" reflections        999
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 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.= 0.907 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  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.26993403    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                41.5
Norm of Geom. positional gradient                78.6
Norm of X_ray B-factor gradient                  137.
Norm of Geom. B-factor gradient                 0.211E+05
Product of X_ray and Geom posit. gradients     -0.104E+08
 Cosine of angle between them                      -0.327
Product of X_ray and Geom B-fact gradients     -0.404E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7059E+06 GEOM=     0.2584E+05 TOTAL=     0.7317E+06
 function value    731738.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.770     1.644
Bond angles  : others                          3242     2.339     1.582
Torsion angles, period  1. refined              184     7.023     5.000
Torsion angles, period  2. refined               90    37.180    22.778
Torsion angles, period  3. refined              268    14.336    15.000
Torsion angles, period  4. refined                9    10.881    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   307     0.269     0.200
VDW repulsions.others                          1345     0.233     0.200
VDW; torsion: refined_atoms                     709     0.171     0.200
VDW; torsion.others                             713     0.080     0.200
HBOND: refined_atoms                            239     0.206     0.200
HBOND.others                                      2     0.044     0.200
VDW repulsions: symmetry: refined_atoms          10     0.233     0.200
VDW repulsions: symmetry: others                 26     0.194     0.200
HBOND: symmetry: refined_atoms                   23     0.200     0.200
HBOND: symmetry: others                           1     0.072     0.200
M. chain bond B values: refined atoms           745     1.573     1.222
M. chain bond B values: others                  745     1.572     1.222
M. chain angle B values: refined atoms          926     2.522     1.814
M. chain angle B values: others                 927     2.521     1.813
S. chain bond B values: refined atoms           811     2.708     1.585
S. chain bond B values: others                  810     2.704     1.584
S. chain angle B values: refined atoms         1177     4.278     2.222
S. chain angle B values: others                1178     4.276     2.221
Long range B values: refined atoms             1862     7.093    17.244
Long range B values: others                    1767     6.764    15.923
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.8296
Partial structure    1: scale =     0.3797, B  =   49.5549
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2555 100.00   472.1   479.3  0.15  0.16     138   475.5   491.1  0.18  0.20
 0.116    4347 100.00   341.6   327.7  0.16  0.15     232   333.5   318.5  0.21  0.19
 0.193    5525  99.97   225.7   214.6  0.16  0.14     283   227.5   217.4  0.22  0.19
 0.270    6442 100.00   147.8   154.4  0.22  0.16     345   145.6   152.2  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1791   0.932    764   0.842   2555   0.905  0.964  0.9720  0.9737  0.9334  0.9434
  0.1161   3579   0.892    768   0.789   4347   0.874  0.994  0.9561  0.9657  0.9209  0.9470
  0.1931   4752   0.868    773   0.755   5525   0.852  1.006  0.9430  0.9566  0.8856  0.9369
  0.2701   5673   0.834    776   0.752   6449   0.824  0.898  0.9340  0.9424  0.8810  0.9052
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18876
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0264
Overall R factor                     =     0.1692
Free R factor                        =     0.2115
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9469
Overall weighted R factor            =     0.1512
Free weighted R factor               =     0.1921
Overall weighted R2 factor           =     0.1798
Free weighted R2 factor              =     0.2322
Average correlation coefficient      =     0.9293
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9374
Cruickshanks DPI for coordinate error=     0.1236
DPI based on free R factor           =     0.1208
Overall figure of merit              =     0.8547
ML based su of positional parameters =     0.0781
ML based su of thermal parameters    =     2.5194
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100849.58       25835.844       731738.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31008175    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712747.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0414
Partial structure    1: scale =     0.3790, B  =   49.0326
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1680
Free R factor                        =     0.2099
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9507
Average correlation coefficient      =     0.9325
Overall figure of merit              =     0.8695
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100380.20       10129.920       712747.25       731738.63    


     CGMAT cycle number =      3

 Weight matrix   0.31840691    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709967.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0085
Partial structure    1: scale =     0.3786, B  =   46.2895
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2081
Average Fourier shell correlation    =     0.9611
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9346
Overall figure of merit              =     0.8717
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100068.57       9531.4160       709967.50       712747.25    


     CGMAT cycle number =      4

 Weight matrix   0.32460967    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708906.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0377
Partial structure    1: scale =     0.3795, B  =   46.1418
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2071
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9352
Overall figure of merit              =     0.8730
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99936.992       9391.5430       708906.69       709967.50    


     CGMAT cycle number =      5

 Weight matrix   0.32654145    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708483.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0076
Partial structure    1: scale =     0.3797, B  =   46.1436
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1660
Free R factor                        =     0.2067
Average Fourier shell correlation    =     0.9617
AverageFree Fourier shell correlation=     0.9524
Average correlation coefficient      =     0.9356
Overall figure of merit              =     0.8735
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99874.195       9408.2676       708483.81       708906.69    


     CGMAT cycle number =      6

 Weight matrix   0.32816678    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708274.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0004
Partial structure    1: scale =     0.3797, B  =   46.1272
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1660
Free R factor                        =     0.2063
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8739
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99835.414       9470.6738       708274.81       708483.81    


     CGMAT cycle number =      7

 Weight matrix   0.32905838    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708140.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0035
Partial structure    1: scale =     0.3798, B  =   46.1188
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2062
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9527
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8742
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99811.734       9501.6484       708140.00       708274.81    


     CGMAT cycle number =      8

 Weight matrix   0.32977331    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708071.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0002
Partial structure    1: scale =     0.3798, B  =   46.1187
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1660
Free R factor                        =     0.2063
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9527
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8743
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    99799.898       9516.2891       708071.81       708140.00    


     CGMAT cycle number =      9

 Weight matrix   0.32952136    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708033.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0122
Partial structure    1: scale =     0.3800, B  =   46.2583
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2066
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8743
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    99793.516       9523.0801       708033.88       708071.81    


     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.= 0.917 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.32933658    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                41.0
Norm of Geom. positional gradient                41.0
Norm of X_ray B-factor gradient                  132.
Norm of Geom. B-factor gradient                  131.
Product of X_ray and Geom posit. gradients     -0.163E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.561E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.6985E+06 GEOM=      9527.     TOTAL=     0.7080E+06
 function value    708022.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.855     1.644
Bond angles  : others                          3242     1.487     1.582
Torsion angles, period  1. refined              184     7.009     5.000
Torsion angles, period  2. refined               90    36.873    22.778
Torsion angles, period  3. refined              268    14.204    15.000
Torsion angles, period  4. refined                9    11.902    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   315     0.266     0.200
VDW repulsions.others                          1381     0.205     0.200
VDW; torsion: refined_atoms                     714     0.172     0.200
VDW; torsion.others                             802     0.084     0.200
HBOND: refined_atoms                            226     0.204     0.200
HBOND.others                                      2     0.134     0.200
VDW repulsions: symmetry: refined_atoms           8     0.239     0.200
VDW repulsions: symmetry: others                 23     0.197     0.200
HBOND: symmetry: refined_atoms                   25     0.205     0.200
HBOND: symmetry: others                           1     0.049     0.200
M. chain bond B values: refined atoms           745     1.672     1.294
M. chain bond B values: others                  745     1.669     1.294
M. chain angle B values: refined atoms          926     2.607     1.922
M. chain angle B values: others                 927     2.606     1.922
S. chain bond B values: refined atoms           811     2.980     1.689
S. chain bond B values: others                  810     2.976     1.689
S. chain angle B values: refined atoms         1177     4.686     2.366
S. chain angle B values: others                1178     4.684     2.365
Long range B values: refined atoms             1860     7.223    18.327
Long range B values: others                    1765     6.903    16.894
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0082
Partial structure    1: scale =     0.3800, B  =   46.3157
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2555 100.00   471.4   480.1  0.15  0.16     138   474.8   493.1  0.17  0.19
 0.116    4347 100.00   341.0   326.2  0.16  0.15     232   333.0   317.6  0.21  0.20
 0.193    5525  99.97   225.4   213.7  0.17  0.14     283   227.1   216.5  0.22  0.18
 0.270    6442 100.00   147.6   153.8  0.19  0.15     345   145.4   152.0  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1791   0.941    764   0.853   2555   0.915  0.964  0.9740  0.9752  0.9358  0.9427
  0.1161   3579   0.901    768   0.801   4347   0.883  0.995  0.9589  0.9674  0.9240  0.9464
  0.1931   4752   0.872    773   0.759   5525   0.857  1.007  0.9448  0.9569  0.8883  0.9341
  0.2701   5673   0.876    776   0.801   6449   0.867  0.915  0.9461  0.9574  0.8935  0.9281
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18876
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0264
Overall R factor                     =     0.1661
Free R factor                        =     0.2067
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9526
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1889
Overall weighted R2 factor           =     0.1814
Free weighted R2 factor              =     0.2306
Average correlation coefficient      =     0.9361
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9400
Cruickshanks DPI for coordinate error=     0.1213
DPI based on free R factor           =     0.1181
Overall figure of merit              =     0.8742
ML based su of positional parameters =     0.0706
ML based su of thermal parameters    =     2.2342
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99791.406       9526.8496       708022.94       708033.88    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.917 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_complete_R04_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.855     1.644
Bond angles  : others                          3242     1.487     1.582
Torsion angles, period  1. refined              184     7.002     5.000
Torsion angles, period  2. refined               90    36.873    22.778
Torsion angles, period  3. refined              268    14.197    15.000
Torsion angles, period  4. refined                9    11.904    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   314     0.267     0.200
VDW repulsions.others                          1382     0.205     0.200
VDW; torsion: refined_atoms                     713     0.172     0.200
VDW; torsion.others                             805     0.084     0.200
HBOND: refined_atoms                            225     0.205     0.200
HBOND.others                                      2     0.135     0.200
VDW repulsions: symmetry: refined_atoms           8     0.239     0.200
VDW repulsions: symmetry: others                 22     0.202     0.200
HBOND: symmetry: refined_atoms                   25     0.206     0.200
HBOND: symmetry: others                           1     0.047     0.200
M. chain bond B values: refined atoms           745     1.672     1.294
M. chain bond B values: others                  745     1.670     1.294
M. chain angle B values: refined atoms          926     2.607     1.922
M. chain angle B values: others                 927     2.606     1.922
S. chain bond B values: refined atoms           811     2.980     1.689
S. chain bond B values: others                  810     2.976     1.689
S. chain angle B values: refined atoms         1177     4.687     2.366
S. chain angle B values: others                1178     4.685     2.365
Long range B values: refined atoms             1858     7.190    18.267
Long range B values: others                    1763     6.864    16.829
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0067
Partial structure    1: scale =     0.3799, B  =   46.3554
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2555 100.00   471.4   480.1  0.15  0.16     138   474.8   493.2  0.17  0.19
 0.116    4347 100.00   341.0   326.2  0.16  0.15     232   333.0   317.6  0.21  0.20
 0.193    5525  99.97   225.4   213.7  0.17  0.14     283   227.1   216.5  0.22  0.18
 0.270    6442 100.00   147.6   153.8  0.19  0.15     345   145.4   152.0  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1791   0.941    764   0.853   2555   0.915  0.964  0.9740  0.9752  0.9358  0.9427
  0.1161   3579   0.901    768   0.801   4347   0.883  0.995  0.9588  0.9673  0.9237  0.9464
  0.1931   4752   0.872    773   0.759   5525   0.856  1.007  0.9447  0.9568  0.8882  0.9341
  0.2701   5673   0.876    776   0.801   6449   0.867  0.915  0.9461  0.9575  0.8936  0.9283
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18876
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0264
Overall R factor                     =     0.1661
Free R factor                        =     0.2068
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9525
Overall weighted R factor            =     0.1512
Free weighted R factor               =     0.1890
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2309
Average correlation coefficient      =     0.9361
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9399
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1181
Overall figure of merit              =     0.8743
ML based su of positional parameters =     0.0706
ML based su of thermal parameters    =     2.2342
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.68
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1692   0.2115   0.855      100850.    5488.8   0.0120  0.882   1.770  1.023   0.084
       1   0.1680   0.2099   0.870      100380.    5472.6   0.0122  0.885   1.760  1.016   0.085
       2   0.1666   0.2081   0.872      100069.    5462.3   0.0132  0.957   1.804  1.042   0.088
       3   0.1662   0.2071   0.873       99937.    5457.4   0.0133  0.969   1.824  1.054   0.088
       4   0.1660   0.2067   0.873       99874.    5454.5   0.0134  0.976   1.837  1.062   0.089
       5   0.1660   0.2063   0.874       99835.    5452.9   0.0134  0.977   1.844  1.066   0.089
       6   0.1659   0.2062   0.874       99812.    5452.3   0.0134  0.979   1.849  1.069   0.089
       7   0.1660   0.2063   0.874       99800.    5452.2   0.0134  0.979   1.851  1.070   0.089
       8   0.1661   0.2066   0.874       99794.    5452.1   0.0135  0.980   1.854  1.072   0.090
       9   0.1661   0.2067   0.874       99791.    5452.5   0.0135  0.981   1.855  1.072   0.090
      10   0.1661   0.2068   0.874       99791.    5452.9   0.0135  0.980   1.855  1.072   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1692   0.1661
             R free    0.2115   0.2068
     Rms BondLength    0.0120   0.0135
      Rms BondAngle    1.7695   1.8549
     Rms ChirVolume    0.0842   0.0896
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.6s System:    0.1s Elapsed:     0:45