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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: 16:06:20 


 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 1.77     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_1-78A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-77A.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_1-77A.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       0.0798
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7700
  Estimated number of reflections :      26680
  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  1.7700

  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_1-78A.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=   2.059 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.212 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.851 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=   2.208 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=   2.425 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=   2.405 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=   2.118 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       1061
Number of   all  reflections      20892
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          20892

   Current auto weighting coefficient =    6.9246206    

 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.= 0.911 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  162
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  162
 Weight matrix   0.26999712    
 Actual weight    6.9246206      is applied to the X-ray term
Norm of X_ray positional gradient                34.9
Norm of Geom. positional gradient                79.5
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.119E+08
 Cosine of angle between them                      -0.444
Product of X_ray and Geom B-fact gradients     -0.394E+08
 Cosine of angle between them                      -0.915


Residuals: XRAY=     0.7275E+06 GEOM=     0.1334E+05 TOTAL=     0.7408E+06
 function value    740822.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.816     1.644
Bond angles  : others                          3238     2.354     1.580
Torsion angles, period  1. refined              185     6.884     5.000
Torsion angles, period  2. refined               90    35.726    22.778
Torsion angles, period  3. refined              268    13.213    15.000
Torsion angles, period  4. refined                9    12.422    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   299     0.244     0.200
VDW repulsions.others                          1327     0.220     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             721     0.080     0.200
HBOND: refined_atoms                            214     0.201     0.200
HBOND.others                                      1     0.058     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 19     0.215     0.200
HBOND: symmetry: refined_atoms                   23     0.183     0.200
M. chain bond B values: refined atoms           746     1.641     1.314
M. chain bond B values: others                  746     1.639     1.314
M. chain angle B values: refined atoms          929     2.585     1.957
M. chain angle B values: others                 930     2.584     1.957
S. chain bond B values: refined atoms           811     2.862     1.691
S. chain bond B values: others                  810     2.857     1.691
S. chain angle B values: refined atoms         1177     4.441     2.377
S. chain angle B values: others                1178     4.439     2.377
Long range B values: refined atoms             1840     6.846    18.165
Long range B values: others                    1751     6.599    16.809
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =    0.0396
Partial structure    1: scale =     0.3841, B  =   44.6841
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2712 100.00   467.7   475.5  0.16  0.17     124   460.2   471.8  0.20  0.22
 0.120    4549 100.00   327.4   313.6  0.17  0.15     255   328.3   303.6  0.22  0.20
 0.200    5776  99.97   219.0   206.3  0.16  0.14     310   229.3   216.5  0.20  0.17
 0.279    6783 100.00   134.3   142.1  0.21  0.16     372   134.7   143.0  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0404   1915   0.914    797   0.807   2712   0.882  0.952  0.9614  0.9697  0.9075  0.9404
  0.1201   3747   0.872    802   0.769   4549   0.854  0.993  0.9455  0.9593  0.8896  0.9422
  0.1997   4981   0.880    795   0.775   5776   0.866  1.023  0.9526  0.9604  0.9042  0.9398
  0.2794   5989   0.809    803   0.727   6792   0.799  0.886  0.9284  0.9412  0.8716  0.9226
 $$
Resolution limits                    =     41.964     1.770
Number of used reflections           =      19829
Percentage observed                  =    99.9856
Percentage of free reflections       =     5.0790
Overall R factor                     =     0.1703
Free R factor                        =     0.2208
Average Fourier shell correlation    =     0.9548
AverageFree Fourier shell correlation=     0.9434
Overall weighted R factor            =     0.1549
Free weighted R factor               =     0.1994
Overall weighted R2 factor           =     0.1874
Free weighted R2 factor              =     0.2365
Average correlation coefficient      =     0.9346
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9254
Cruickshanks DPI for coordinate error=     0.1176
DPI based on free R factor           =     0.1210
Overall figure of merit              =     0.8425
ML based su of positional parameters =     0.0776
ML based su of thermal parameters    =     2.4581
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    105056.71       13344.938       740822.81      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.29877108    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    733113.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0914
Partial structure    1: scale =     0.3840, B  =   44.7180
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1704
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9578
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9345
Overall figure of merit              =     0.8562
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    104629.74       8591.9727       733113.25       740822.81    


     CGMAT cycle number =      3

 Weight matrix   0.30094841    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732779.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0680
Partial structure    1: scale =     0.3842, B  =   44.6345
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1700
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9470
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8570
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    104555.62       8771.7051       732779.69       733113.25    


     CGMAT cycle number =      4

 Weight matrix   0.30125237    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732729.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0607
Partial structure    1: scale =     0.3841, B  =   44.5384
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1700
Free R factor                        =     0.2194
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8571
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    104541.73       8817.2988       732729.13       732779.69    


     CGMAT cycle number =      5

 Weight matrix   0.30160660    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732669.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0592
Partial structure    1: scale =     0.3840, B  =   44.5744
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1699
Free R factor                        =     0.2193
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    104531.06       8831.7852       732669.75       732729.13    


     CGMAT cycle number =      6

 Weight matrix   0.30148041    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732674.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0595
Partial structure    1: scale =     0.3841, B  =   44.6301
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1699
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9350
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03

 fvalues    104529.49       8834.2764       732661.31       732669.75    


     CGMAT cycle number =      7

 Weight matrix   0.30138236    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732669.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0575
Partial structure    1: scale =     0.3841, B  =   44.6694
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1700
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    104528.07       8830.5371       732647.81       732661.31    


     CGMAT cycle number =      8

 Weight matrix   0.30135623    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732644.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0580
Partial structure    1: scale =     0.3842, B  =   44.7746
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1700
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    104528.14       8826.7871       732644.56       732647.81    


     CGMAT cycle number =      9

 Weight matrix   0.30117315    
 Actual weight    6.9246206      is applied to the X-ray term


 function value    732657.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0602
Partial structure    1: scale =     0.3841, B  =   44.7873
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1700
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    104531.05       8816.1426       732646.94       732644.56    
 fvalues    104531.05       8816.1426       732646.94       732654.00    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.921 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  162
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  162
 Weight matrix   0.30135289    
 Actual weight    6.9246206      is applied to the X-ray term
Norm of X_ray positional gradient                37.9
Norm of Geom. positional gradient                37.9
Norm of X_ray B-factor gradient                  120.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.470E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.7238E+06 GEOM=      8818.     TOTAL=     0.7326E+06
 function value    732643.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.809     1.644
Bond angles  : others                          3238     1.483     1.580
Torsion angles, period  1. refined              185     6.855     5.000
Torsion angles, period  2. refined               90    35.709    22.778
Torsion angles, period  3. refined              268    13.229    15.000
Torsion angles, period  4. refined                9    12.266    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1367     0.190     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             789     0.083     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.005     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 23     0.179     0.200
HBOND: symmetry: refined_atoms                   23     0.185     0.200
M. chain bond B values: refined atoms           746     1.648     1.326
M. chain bond B values: others                  746     1.646     1.326
M. chain angle B values: refined atoms          929     2.591     1.975
M. chain angle B values: others                 930     2.590     1.975
S. chain bond B values: refined atoms           811     2.876     1.704
S. chain bond B values: others                  810     2.871     1.704
S. chain angle B values: refined atoms         1177     4.455     2.397
S. chain angle B values: others                1178     4.453     2.396
Long range B values: refined atoms             1838     6.837    18.282
Long range B values: others                    1748     6.527    16.889
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0592
Partial structure    1: scale =     0.3842, B  =   44.8278
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2712 100.00   468.0   476.1  0.16  0.17     124   460.5   472.3  0.20  0.21
 0.120    4549 100.00   327.6   313.7  0.17  0.15     255   328.5   304.4  0.22  0.20
 0.200    5776  99.97   219.1   206.4  0.16  0.14     310   229.5   216.9  0.20  0.17
 0.279    6783 100.00   134.4   142.2  0.21  0.16     372   134.8   143.0  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0404   1915   0.926    797   0.824   2712   0.896  0.954  0.9644  0.9723  0.9073  0.9405
  0.1201   3747   0.875    802   0.773   4549   0.857  0.993  0.9472  0.9603  0.8924  0.9426
  0.1997   4981   0.884    795   0.779   5776   0.869  1.023  0.9538  0.9616  0.9060  0.9409
  0.2794   5989   0.842    803   0.758   6792   0.832  0.894  0.9358  0.9480  0.8740  0.9224
 $$
Resolution limits                    =     41.964     1.770
Number of used reflections           =      19829
Percentage observed                  =    99.9856
Percentage of free reflections       =     5.0790
Overall R factor                     =     0.1700
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9471
Overall weighted R factor            =     0.1548
Free weighted R factor               =     0.1980
Overall weighted R2 factor           =     0.1871
Free weighted R2 factor              =     0.2349
Average correlation coefficient      =     0.9349
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9265
Cruickshanks DPI for coordinate error=     0.1174
DPI based on free R factor           =     0.1201
Overall figure of merit              =     0.8572
ML based su of positional parameters =     0.0734
ML based su of thermal parameters    =     2.3010
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    104529.17       8818.1289       732643.00       732654.00    

    ****                              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.= 0.921 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_step0-01A_R00_1-77A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.809     1.644
Bond angles  : others                          3238     1.483     1.580
Torsion angles, period  1. refined              185     6.852     5.000
Torsion angles, period  2. refined               90    35.703    22.778
Torsion angles, period  3. refined              268    13.232    15.000
Torsion angles, period  4. refined                9    12.267    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1363     0.190     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             792     0.083     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 23     0.179     0.200
HBOND: symmetry: refined_atoms                   23     0.185     0.200
M. chain bond B values: refined atoms           746     1.648     1.326
M. chain bond B values: others                  746     1.645     1.326
M. chain angle B values: refined atoms          929     2.591     1.975
M. chain angle B values: others                 930     2.590     1.975
S. chain bond B values: refined atoms           811     2.877     1.705
S. chain bond B values: others                  810     2.872     1.704
S. chain angle B values: refined atoms         1177     4.455     2.397
S. chain angle B values: others                1178     4.454     2.396
Long range B values: refined atoms             1838     6.839    18.284
Long range B values: others                    1748     6.528    16.890
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0417, B  =   -0.0617
Partial structure    1: scale =     0.3842, B  =   44.8203
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2712 100.00   468.0   476.1  0.16  0.17     124   460.5   472.3  0.20  0.21
 0.120    4549 100.00   327.6   313.7  0.17  0.15     255   328.5   304.4  0.22  0.20
 0.200    5776  99.97   219.1   206.4  0.16  0.14     310   229.5   216.9  0.20  0.17
 0.279    6783 100.00   134.4   142.2  0.21  0.16     372   134.8   143.0  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0404   1915   0.926    797   0.824   2712   0.896  0.954  0.9644  0.9723  0.9072  0.9405
  0.1201   3747   0.875    802   0.773   4549   0.857  0.993  0.9472  0.9603  0.8926  0.9426
  0.1997   4981   0.884    795   0.779   5776   0.869  1.023  0.9539  0.9616  0.9061  0.9409
  0.2794   5989   0.842    803   0.758   6792   0.832  0.894  0.9358  0.9480  0.8740  0.9224
 $$
Resolution limits                    =     41.964     1.770
Number of used reflections           =      19829
Percentage observed                  =    99.9856
Percentage of free reflections       =     5.0790
Overall R factor                     =     0.1700
Free R factor                        =     0.2190
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9472
Overall weighted R factor            =     0.1548
Free weighted R factor               =     0.1979
Overall weighted R2 factor           =     0.1871
Free weighted R2 factor              =     0.2348
Average correlation coefficient      =     0.9349
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9265
Cruickshanks DPI for coordinate error=     0.1174
DPI based on free R factor           =     0.1200
Overall figure of merit              =     0.8572
ML based su of positional parameters =     0.0734
ML based su of thermal parameters    =     2.3010
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.80
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1703   0.2208   0.842      105057.    5791.9   0.0123  0.919   1.816  1.049   0.085
       1   0.1704   0.2198   0.856      104630.    5781.4   0.0117  0.873   1.773  1.024   0.084
       2   0.1700   0.2195   0.857      104556.    5779.1   0.0122  0.912   1.797  1.038   0.085
       3   0.1700   0.2194   0.857      104542.    5778.6   0.0123  0.916   1.804  1.043   0.085
       4   0.1699   0.2193   0.857      104531.    5778.1   0.0123  0.917   1.807  1.044   0.085
       5   0.1699   0.2191   0.857      104531.    5778.0   0.0123  0.918   1.808  1.045   0.086
       6   0.1700   0.2191   0.857      104531.    5778.0   0.0123  0.917   1.809  1.045   0.086
       7   0.1700   0.2191   0.857      104528.    5778.1   0.0123  0.917   1.809  1.046   0.086
       8   0.1700   0.2191   0.857      104531.    5778.2   0.0123  0.917   1.809  1.045   0.086
       9   0.1700   0.2191   0.857      104529.    5778.0   0.0123  0.917   1.809  1.045   0.086
      10   0.1700   0.2190   0.857      104529.    5777.8   0.0123  0.917   1.809  1.045   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1703   0.1700
             R free    0.2208   0.2190
     Rms BondLength    0.0123   0.0123
      Rms BondAngle    1.8158   1.8092
     Rms ChirVolume    0.0846   0.0857
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.9s System:    0.1s Elapsed:     0:48