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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 13:37:18 


 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 1.91     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-01A_R00_1-92A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-91A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-91A.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       0.0685
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9100
  Estimated number of reflections :      21862
  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  1.9100

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_step0-01A_R00_1-92A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   1.998 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=   2.202 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=   1.853 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=   2.369 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=   2.423 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=   2.113 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        849
Number of   all  reflections      16718
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16718

   Current auto weighting coefficient =    7.2746773    

 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.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    72   72  153
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    72   72  153
 Weight matrix   0.21312547    
 Actual weight    7.2746773      is applied to the X-ray term
Norm of X_ray positional gradient                31.4
Norm of Geom. positional gradient                77.5
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  105.
Product of X_ray and Geom posit. gradients     -0.855E+07
 Cosine of angle between them                      -0.363
Product of X_ray and Geom B-fact gradients     -0.335E+08
 Cosine of angle between them                      -0.922


Residuals: XRAY=     0.6309E+06 GEOM=     0.1261E+05 TOTAL=     0.6435E+06
 function value    643459.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.704     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     7.022     5.000
Torsion angles, period  2. refined               90    36.776    22.778
Torsion angles, period  3. refined              268    14.363    15.000
Torsion angles, period  4. refined                9    11.484    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   302     0.242     0.200
VDW repulsions.others                          1335     0.220     0.200
VDW; torsion: refined_atoms                     712     0.170     0.200
VDW; torsion.others                             706     0.080     0.200
HBOND: refined_atoms                            230     0.206     0.200
Metal-ion: refined_atoms                          1     0.002     0.200
VDW repulsions: symmetry: refined_atoms           9     0.214     0.200
VDW repulsions: symmetry: others                 25     0.199     0.200
HBOND: symmetry: refined_atoms                   21     0.210     0.200
M. chain bond B values: refined atoms           746     1.525     1.209
M. chain bond B values: others                  746     1.524     1.209
M. chain angle B values: refined atoms          929     2.466     1.799
M. chain angle B values: others                 930     2.465     1.799
S. chain bond B values: refined atoms           811     2.440     1.536
S. chain bond B values: others                  810     2.437     1.536
S. chain angle B values: refined atoms         1177     3.864     2.161
S. chain angle B values: others                1178     3.862     2.160
Long range B values: refined atoms             1853     6.530    16.891
Long range B values: others                    1751     6.191    15.454
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0980
Partial structure    1: scale =     0.3800, B  =   46.7536
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2190 100.00   482.2   485.5  0.16  0.17      98   478.3   484.1  0.20  0.22
 0.103    3668 100.00   390.1   372.9  0.16  0.15     182   389.9   366.2  0.22  0.20
 0.172    4603  99.96   249.2   244.9  0.16  0.13     275   266.0   255.4  0.22  0.19
 0.240    5401 100.00   191.6   191.5  0.16  0.13     294   196.3   197.3  0.23  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0348   1507   0.909    683   0.805   2190   0.876  0.959  0.9607  0.9686  0.9134  0.9411
  0.1031   2980   0.881    688   0.769   3668   0.860  0.996  0.9456  0.9622  0.8757  0.9441
  0.1715   3920   0.863    683   0.768   4603   0.849  0.976  0.9444  0.9566  0.8879  0.9397
  0.2399   4713   0.863    693   0.740   5406   0.847  0.957  0.9399  0.9549  0.8642  0.9378
 $$
Resolution limits                    =     41.964     1.910
Number of used reflections           =      15867
Percentage observed                  =    99.9821
Percentage of free reflections       =     5.0790
Overall R factor                     =     0.1597
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9450
Overall weighted R factor            =     0.1495
Free weighted R factor               =     0.2014
Overall weighted R2 factor           =     0.1816
Free weighted R2 factor              =     0.2434
Average correlation coefficient      =     0.9403
Overall correlation coefficient      =     0.9550
Free correlation coefficient         =     0.9119
Cruickshanks DPI for coordinate error=     0.1440
DPI based on free R factor           =     0.1432
Overall figure of merit              =     0.8548
ML based su of positional parameters =     0.0896
ML based su of thermal parameters    =     2.9839
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    86718.766       12608.100       643459.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.22028285    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637538.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1242
Partial structure    1: scale =     0.3801, B  =   46.9629
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    86520.734       8127.5430       637538.00       643459.19    


     CGMAT cycle number =      3

 Weight matrix   0.22066431    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637430.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1316
Partial structure    1: scale =     0.3801, B  =   46.8066
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1592
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    86501.055       8163.7012       637430.94       637538.00    


     CGMAT cycle number =      4

 Weight matrix   0.22076862    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637390.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1286
Partial structure    1: scale =     0.3802, B  =   46.8400
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    86493.047       8181.1367       637390.13       637430.94    


     CGMAT cycle number =      5

 Weight matrix   0.22072476    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637353.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1306
Partial structure    1: scale =     0.3802, B  =   46.8321
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    86487.813       8182.0869       637353.00       637390.13    


     CGMAT cycle number =      6

 Weight matrix   0.22068661    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637314.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1351
Partial structure    1: scale =     0.3803, B  =   46.6724
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    86483.031       8178.0752       637314.19       637353.00    


     CGMAT cycle number =      7

 Weight matrix   0.22042441    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637315.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1399
Partial structure    1: scale =     0.3803, B  =   46.6799
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    86483.414       8171.9185       637310.88       637314.19    


     CGMAT cycle number =      8

 Weight matrix   0.22000434    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637339.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1444
Partial structure    1: scale =     0.3804, B  =   46.7475
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    86488.570       8166.9756       637331.25       637310.88    
 fvalues    86488.570       8166.9756       637331.25       637343.44    


     CGMAT cycle number =      9

 Weight matrix   0.21985006    
 Actual weight    7.2746773      is applied to the X-ray term


 function value    637352.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1338
Partial structure    1: scale =     0.3804, B  =   46.7385
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    86489.813       8157.1021       637342.63       637343.44    


     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.= 0.952 id.= 3.000 dev= -2.05 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    72   72  153
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    72   72  153
 Weight matrix   0.21984591    
 Actual weight    7.2746773      is applied to the X-ray term
Norm of X_ray positional gradient                31.1
Norm of Geom. positional gradient                31.1
Norm of X_ray B-factor gradient                  105.
Norm of Geom. B-factor gradient                  110.
Product of X_ray and Geom posit. gradients     -0.935E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.367E+08
 Cosine of angle between them                      -0.980


Residuals: XRAY=     0.6292E+06 GEOM=      8154.     TOTAL=     0.6373E+06
 function value    637332.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.710     1.644
Bond angles  : others                          3238     1.425     1.580
Torsion angles, period  1. refined              185     7.015     5.000
Torsion angles, period  2. refined               90    36.767    22.778
Torsion angles, period  3. refined              268    14.151    15.000
Torsion angles, period  4. refined                9    11.481    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.241     0.200
VDW repulsions.others                          1365     0.191     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             784     0.083     0.200
HBOND: refined_atoms                            232     0.208     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 24     0.194     0.200
HBOND: symmetry: refined_atoms                   21     0.211     0.200
M. chain bond B values: refined atoms           746     1.536     1.215
M. chain bond B values: others                  746     1.534     1.215
M. chain angle B values: refined atoms          929     2.480     1.808
M. chain angle B values: others                 930     2.479     1.807
S. chain bond B values: refined atoms           811     2.471     1.543
S. chain bond B values: others                  810     2.468     1.543
S. chain angle B values: refined atoms         1177     3.892     2.170
S. chain angle B values: others                1178     3.891     2.170
Long range B values: refined atoms             1857     6.569    17.045
Long range B values: others                    1755     6.253    15.607
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1318
Partial structure    1: scale =     0.3803, B  =   46.7916
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2190 100.00   482.4   485.9  0.16  0.17      98   478.5   483.0  0.20  0.22
 0.103    3668 100.00   390.3   372.9  0.16  0.15     182   390.1   365.8  0.22  0.20
 0.172    4603  99.96   249.3   244.9  0.16  0.13     275   266.1   255.5  0.22  0.19
 0.240    5401 100.00   191.7   191.6  0.16  0.13     294   196.4   197.1  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0348   1507   0.922    683   0.820   2190   0.890  0.959  0.9634  0.9714  0.9124  0.9412
  0.1031   2980   0.885    688   0.773   3668   0.864  0.996  0.9474  0.9633  0.8784  0.9444
  0.1715   3920   0.865    683   0.769   4603   0.851  0.976  0.9455  0.9571  0.8904  0.9399
  0.2399   4713   0.866    693   0.743   5406   0.850  0.957  0.9410  0.9563  0.8653  0.9397
 $$
Resolution limits                    =     41.964     1.910
Number of used reflections           =      15867
Percentage observed                  =    99.9821
Percentage of free reflections       =     5.0790
Overall R factor                     =     0.1591
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9464
Overall weighted R factor            =     0.1491
Free weighted R factor               =     0.2005
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2419
Average correlation coefficient      =     0.9410
Overall correlation coefficient      =     0.9552
Free correlation coefficient         =     0.9129
Cruickshanks DPI for coordinate error=     0.1435
DPI based on free R factor           =     0.1427
Overall figure of merit              =     0.8590
ML based su of positional parameters =     0.0881
ML based su of thermal parameters    =     2.9448
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    86488.930       8153.8789       637332.94       637342.63    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.953 id.= 3.000 dev= -2.05 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-91A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.710     1.644
Bond angles  : others                          3238     1.425     1.580
Torsion angles, period  1. refined              185     7.013     5.000
Torsion angles, period  2. refined               90    36.765    22.778
Torsion angles, period  3. refined              268    14.125    15.000
Torsion angles, period  4. refined                9    11.473    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.241     0.200
VDW repulsions.others                          1370     0.191     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             787     0.083     0.200
HBOND: refined_atoms                            232     0.208     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 24     0.194     0.200
HBOND: symmetry: refined_atoms                   21     0.212     0.200
M. chain bond B values: refined atoms           746     1.536     1.215
M. chain bond B values: others                  746     1.535     1.215
M. chain angle B values: refined atoms          929     2.481     1.809
M. chain angle B values: others                 930     2.479     1.808
S. chain bond B values: refined atoms           811     2.471     1.544
S. chain bond B values: others                  810     2.468     1.543
S. chain angle B values: refined atoms         1177     3.892     2.171
S. chain angle B values: others                1178     3.890     2.171
Long range B values: refined atoms             1857     6.555    17.028
Long range B values: others                    1755     6.238    15.588
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =   -0.1341
Partial structure    1: scale =     0.3803, B  =   46.8347
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2190 100.00   482.5   485.9  0.16  0.17      98   478.6   483.1  0.20  0.22
 0.103    3668 100.00   390.4   372.8  0.16  0.15     182   390.2   365.8  0.22  0.20
 0.172    4603  99.96   249.4   244.9  0.16  0.13     275   266.2   255.4  0.22  0.19
 0.240    5401 100.00   191.7   191.6  0.16  0.13     294   196.4   197.0  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0348   1507   0.922    683   0.820   2190   0.890  0.959  0.9634  0.9714  0.9123  0.9412
  0.1031   2980   0.885    688   0.773   3668   0.864  0.996  0.9475  0.9633  0.8786  0.9444
  0.1715   3920   0.865    683   0.769   4603   0.850  0.976  0.9455  0.9570  0.8905  0.9399
  0.2399   4713   0.866    693   0.743   5406   0.850  0.957  0.9410  0.9563  0.8654  0.9397
 $$
Resolution limits                    =     41.964     1.910
Number of used reflections           =      15867
Percentage observed                  =    99.9821
Percentage of free reflections       =     5.0790
Overall R factor                     =     0.1590
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9464
Overall weighted R factor            =     0.1491
Free weighted R factor               =     0.2004
Overall weighted R2 factor           =     0.1814
Free weighted R2 factor              =     0.2418
Average correlation coefficient      =     0.9411
Overall correlation coefficient      =     0.9552
Free correlation coefficient         =     0.9130
Cruickshanks DPI for coordinate error=     0.1435
DPI based on free R factor           =     0.1427
Overall figure of merit              =     0.8589
ML based su of positional parameters =     0.0881
ML based su of thermal parameters    =     2.9448
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.53
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1597   0.2166   0.855       86719.    4806.2   0.0110  0.816   1.704  0.990   0.083
       1   0.1596   0.2157   0.859       86521.    4801.5   0.0109  0.801   1.687  0.981   0.083
       2   0.1592   0.2156   0.859       86501.    4800.9   0.0111  0.821   1.699  0.989   0.084
       3   0.1591   0.2156   0.859       86493.    4800.6   0.0111  0.824   1.704  0.991   0.084
       4   0.1591   0.2156   0.859       86488.    4800.5   0.0112  0.825   1.706  0.993   0.083
       5   0.1590   0.2156   0.859       86483.    4800.3   0.0112  0.825   1.707  0.993   0.083
       6   0.1590   0.2157   0.859       86484.    4800.5   0.0112  0.825   1.708  0.994   0.083
       7   0.1590   0.2159   0.859       86488.    4801.2   0.0111  0.824   1.709  0.994   0.083
       8   0.1590   0.2159   0.859       86491.    4801.3   0.0111  0.824   1.709  0.995   0.083
       9   0.1591   0.2159   0.859       86489.    4801.3   0.0111  0.824   1.710  0.995   0.083
      10   0.1590   0.2159   0.859       86494.    4801.4   0.0111  0.823   1.710  0.995   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1597   0.1590
             R free    0.2166   0.2159
     Rms BondLength    0.0110   0.0111
      Rms BondAngle    1.7035   1.7098
     Rms ChirVolume    0.0833   0.0833
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.7s System:    0.2s Elapsed:     0:47