###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 14:27:38 


 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 1.85     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_1-86A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-85A.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_1-85A.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       0.0730
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8500
  Estimated number of reflections :      24012
  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  1.8500

  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_1-86A.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=   2.031 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=   2.218 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=   1.864 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=   2.220 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=   2.385 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=   2.431 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=   2.138 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        924
Number of   all  reflections      18355
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          18355

   Current auto weighting coefficient =    7.1245985    

 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.= 0.927 id.= 3.000 dev= -2.07 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                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Weight matrix   0.23830856    
 Actual weight    7.1245985      is applied to the X-ray term
Norm of X_ray positional gradient                32.6
Norm of Geom. positional gradient                78.3
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  110.
Product of X_ray and Geom posit. gradients     -0.992E+07
 Cosine of angle between them                      -0.402
Product of X_ray and Geom B-fact gradients     -0.367E+08
 Cosine of angle between them                      -0.938


Residuals: XRAY=     0.6702E+06 GEOM=     0.1288E+05 TOTAL=     0.6831E+06
 function value    683056.38    

-------------------------------------------------------------------------------
             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     1.747     1.644
Bond angles  : others                          3238     2.348     1.580
Torsion angles, period  1. refined              185     6.989     5.000
Torsion angles, period  2. refined               90    35.927    22.778
Torsion angles, period  3. refined              268    13.392    15.000
Torsion angles, period  4. refined                9    11.344    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     0.242     0.200
VDW repulsions.others                          1329     0.220     0.200
VDW; torsion: refined_atoms                     714     0.172     0.200
VDW; torsion.others                             719     0.079     0.200
HBOND: refined_atoms                            226     0.207     0.200
VDW repulsions: symmetry: refined_atoms          10     0.206     0.200
VDW repulsions: symmetry: others                 24     0.208     0.200
HBOND: symmetry: refined_atoms                   19     0.208     0.200
M. chain bond B values: refined atoms           746     1.567     1.247
M. chain bond B values: others                  746     1.565     1.247
M. chain angle B values: refined atoms          929     2.508     1.856
M. chain angle B values: others                 930     2.506     1.855
S. chain bond B values: refined atoms           811     2.574     1.592
S. chain bond B values: others                  810     2.573     1.592
S. chain angle B values: refined atoms         1177     4.049     2.239
S. chain angle B values: others                1178     4.047     2.238
Long range B values: refined atoms             1848     6.692    17.261
Long range B values: others                    1753     6.395    15.881
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =    0.0131
Partial structure    1: scale =     0.3766, B  =   46.5799
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2393 100.00   475.9   482.8  0.16  0.17     109   473.8   481.7  0.20  0.22
 0.110    4011 100.00   364.3   348.2  0.16  0.15     207   365.7   339.0  0.22  0.20
 0.183    5051  99.96   237.4   229.5  0.16  0.14     295   252.1   239.8  0.21  0.18
 0.256    5970 100.00   168.1   171.4  0.18  0.14     312   169.8   173.8  0.24  0.19
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0370   1666   0.912    727   0.802   2393   0.878  0.955  0.9606  0.9689  0.9056  0.9412
  0.1099   3277   0.878    734   0.774   4011   0.859  0.995  0.9471  0.9617  0.8892  0.9448
  0.1828   4323   0.871    728   0.769   5051   0.856  0.995  0.9482  0.9583  0.8909  0.9385
  0.2557   5235   0.846    739   0.742   5974   0.833  0.929  0.9371  0.9514  0.8696  0.9314
 $$
Resolution limits                    =     41.964     1.850
Number of used reflections           =      17429
Percentage observed                  =    99.9837
Percentage of free reflections       =     5.0346
Overall R factor                     =     0.1638
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9582
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1514
Free weighted R factor               =     0.1988
Overall weighted R2 factor           =     0.1841
Free weighted R2 factor              =     0.2395
Average correlation coefficient      =     0.9379
Overall correlation coefficient      =     0.9557
Free correlation coefficient         =     0.9178
Cruickshanks DPI for coordinate error=     0.1315
DPI based on free R factor           =     0.1319
Overall figure of merit              =     0.8521
ML based su of positional parameters =     0.0838
ML based su of thermal parameters    =     2.7353
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    94065.648       12876.376       683056.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.24869242    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676940.81    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0916
Partial structure    1: scale =     0.3767, B  =   46.6776
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1638
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9382
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    93850.469       8293.9043       676940.81       683056.38    


     CGMAT cycle number =      3

 Weight matrix   0.24918529    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676848.69    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0854
Partial structure    1: scale =     0.3768, B  =   46.6421
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1635
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    93826.266       8374.1641       676848.69       676940.81    


     CGMAT cycle number =      4

 Weight matrix   0.24937692    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676837.63    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0806
Partial structure    1: scale =     0.3768, B  =   46.6974
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1634
Free R factor                        =     0.2154
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    93821.805       8394.9629       676837.63       676848.69    


     CGMAT cycle number =      5

 Weight matrix   0.24948150    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676801.94    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0842
Partial structure    1: scale =     0.3769, B  =   46.7830
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1634
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    93816.430       8397.5420       676801.94       676837.63    


     CGMAT cycle number =      6

 Weight matrix   0.24942504    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676796.56    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0865
Partial structure    1: scale =     0.3770, B  =   46.7554
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1634
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    93815.453       8399.1523       676796.56       676801.94    


     CGMAT cycle number =      7

 Weight matrix   0.24923111    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676807.50    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0885
Partial structure    1: scale =     0.3770, B  =   46.6976
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1634
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    93817.570       8395.7646       676847.88       676796.56    

 fvalues    93817.570       8395.7646       676801.38       676808.25    
 fvalues    93817.570       8395.7646       676801.38       676808.25    


     CGMAT cycle number =      8

 Weight matrix   0.24896674    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676838.63    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0908
Partial structure    1: scale =     0.3770, B  =   46.7933
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1634
Free R factor                        =     0.2155
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    93822.797       8390.8438       676843.69       676808.25    

 fvalues    93822.797       8390.8438       676846.31       676840.63    
 fvalues    93822.797       8390.8438       676846.31       676840.63    


     CGMAT cycle number =      9

 Weight matrix   0.24902169    
 Actual weight    7.1245985      is applied to the X-ray term


 function value    676826.94    

-------------------------------------------------------------------------------
             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 =     0.0407, B  =   -0.0903
Partial structure    1: scale =     0.3770, B  =   46.7988
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1634
Free R factor                        =     0.2155
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    93820.906       8390.6396       676826.94       676840.63    


     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.= 0.941 id.= 3.000 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Weight matrix   0.24881491    
 Actual weight    7.1245985      is applied to the X-ray term
Norm of X_ray positional gradient                33.3
Norm of Geom. positional gradient                33.3
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.107E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.406E+08
 Cosine of angle between them                      -0.990


Residuals: XRAY=     0.6685E+06 GEOM=      8390.     TOTAL=     0.6769E+06
 function value    676854.94    

-------------------------------------------------------------------------------
             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     1.750     1.644
Bond angles  : others                          3238     1.449     1.580
Torsion angles, period  1. refined              185     6.977     5.000
Torsion angles, period  2. refined               90    35.872    22.778
Torsion angles, period  3. refined              268    13.391    15.000
Torsion angles, period  4. refined                9    11.241    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.241     0.200
VDW repulsions.others                          1367     0.192     0.200
VDW; torsion: refined_atoms                     718     0.172     0.200
VDW; torsion.others                             773     0.083     0.200
HBOND: refined_atoms                            227     0.205     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 23     0.195     0.200
HBOND: symmetry: refined_atoms                   20     0.205     0.200
M. chain bond B values: refined atoms           746     1.571     1.256
M. chain bond B values: others                  746     1.569     1.256
M. chain angle B values: refined atoms          929     2.508     1.870
M. chain angle B values: others                 930     2.507     1.870
S. chain bond B values: refined atoms           811     2.609     1.606
S. chain bond B values: others                  810     2.607     1.606
S. chain angle B values: refined atoms         1177     4.098     2.258
S. chain angle B values: others                1178     4.096     2.257
Long range B values: refined atoms             1852     6.724    17.443
Long range B values: others                    1759     6.436    16.126
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0407, B  =   -0.0869
Partial structure    1: scale =     0.3769, B  =   46.7978
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2393 100.00   476.4   483.1  0.16  0.17     109   474.3   482.7  0.20  0.22
 0.110    4011 100.00   364.7   348.3  0.16  0.15     207   366.1   339.4  0.22  0.20
 0.183    5051  99.96   237.7   229.6  0.16  0.13     295   252.4   240.0  0.21  0.18
 0.256    5970 100.00   168.3   171.5  0.18  0.14     312   169.9   174.2  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0370   1666   0.924    727   0.817   2393   0.892  0.957  0.9639  0.9714  0.9066  0.9412
  0.1099   3277   0.881    734   0.778   4011   0.863  0.995  0.9487  0.9628  0.8908  0.9449
  0.1828   4323   0.872    728   0.772   5051   0.858  0.995  0.9490  0.9590  0.8928  0.9394
  0.2557   5235   0.853    739   0.748   5974   0.840  0.929  0.9388  0.9533  0.8705  0.9327
 $$
Resolution limits                    =     41.964     1.850
Number of used reflections           =      17429
Percentage observed                  =    99.9837
Percentage of free reflections       =     5.0346
Overall R factor                     =     0.1634
Free R factor                        =     0.2154
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9472
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.1840
Free weighted R2 factor              =     0.2384
Average correlation coefficient      =     0.9386
Overall correlation coefficient      =     0.9559
Free correlation coefficient         =     0.9188
Cruickshanks DPI for coordinate error=     0.1312
DPI based on free R factor           =     0.1316
Overall figure of merit              =     0.8574
ML based su of positional parameters =     0.0819
ML based su of thermal parameters    =     2.6770
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    93822.313       8389.9639       676848.69       676826.94    

 fvalues    93822.313       8389.9639       676830.63       676836.25    
 fvalues    93822.313       8389.9639       676830.63       676836.25    

    ****                              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.= 0.941 id.= 3.000 dev= -2.06 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_1-85A.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     1.750     1.644
Bond angles  : others                          3238     1.449     1.580
Torsion angles, period  1. refined              185     6.976     5.000
Torsion angles, period  2. refined               90    35.872    22.778
Torsion angles, period  3. refined              268    13.391    15.000
Torsion angles, period  4. refined                9    11.240    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.241     0.200
VDW repulsions.others                          1369     0.191     0.200
VDW; torsion: refined_atoms                     718     0.172     0.200
VDW; torsion.others                             773     0.083     0.200
HBOND: refined_atoms                            228     0.205     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 23     0.195     0.200
HBOND: symmetry: refined_atoms                   20     0.205     0.200
M. chain bond B values: refined atoms           746     1.570     1.256
M. chain bond B values: others                  746     1.569     1.256
M. chain angle B values: refined atoms          929     2.508     1.870
M. chain angle B values: others                 930     2.507     1.870
S. chain bond B values: refined atoms           811     2.609     1.606
S. chain bond B values: others                  810     2.607     1.606
S. chain angle B values: refined atoms         1177     4.098     2.258
S. chain angle B values: others                1178     4.096     2.257
Long range B values: refined atoms             1853     6.725    17.452
Long range B values: others                    1760     6.438    16.136
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0407, B  =   -0.0890
Partial structure    1: scale =     0.3770, B  =   46.8221
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2393 100.00   476.3   483.1  0.16  0.17     109   474.2   482.7  0.20  0.22
 0.110    4011 100.00   364.7   348.3  0.16  0.15     207   366.1   339.5  0.22  0.20
 0.183    5051  99.96   237.6   229.6  0.16  0.13     295   252.4   240.1  0.21  0.18
 0.256    5970 100.00   168.3   171.6  0.18  0.14     312   169.9   174.3  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0370   1666   0.924    727   0.817   2393   0.892  0.957  0.9639  0.9714  0.9067  0.9412
  0.1099   3277   0.881    734   0.778   4011   0.863  0.995  0.9487  0.9628  0.8908  0.9449
  0.1828   4323   0.872    728   0.772   5051   0.858  0.995  0.9490  0.9590  0.8928  0.9394
  0.2557   5235   0.853    739   0.748   5974   0.840  0.929  0.9388  0.9533  0.8705  0.9327
 $$
Resolution limits                    =     41.964     1.850
Number of used reflections           =      17429
Percentage observed                  =    99.9837
Percentage of free reflections       =     5.0346
Overall R factor                     =     0.1634
Free R factor                        =     0.2154
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9472
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.1839
Free weighted R2 factor              =     0.2384
Average correlation coefficient      =     0.9386
Overall correlation coefficient      =     0.9559
Free correlation coefficient         =     0.9188
Cruickshanks DPI for coordinate error=     0.1312
DPI based on free R factor           =     0.1316
Overall figure of merit              =     0.8575
ML based su of positional parameters =     0.0819
ML based su of thermal parameters    =     2.6770
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.17
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1638   0.2159   0.852       94066.    5163.8   0.0117  0.866   1.747  1.013   0.085
       1   0.1638   0.2153   0.857       93850.    5159.4   0.0113  0.841   1.726  1.000   0.085
       2   0.1635   0.2153   0.857       93826.    5159.1   0.0116  0.865   1.740  1.008   0.085
       3   0.1634   0.2154   0.858       93822.    5159.0   0.0117  0.867   1.744  1.011   0.085
       4   0.1634   0.2153   0.858       93816.    5158.7   0.0117  0.867   1.747  1.012   0.085
       5   0.1634   0.2153   0.858       93815.    5158.6   0.0117  0.868   1.749  1.013   0.085
       6   0.1634   0.2153   0.858       93817.    5158.8   0.0117  0.868   1.750  1.013   0.085
       7   0.1634   0.2155   0.857       93823.    5159.3   0.0117  0.868   1.750  1.014   0.085
       8   0.1634   0.2155   0.857       93821.    5159.2   0.0117  0.868   1.750  1.014   0.085
       9   0.1634   0.2154   0.857       93825.    5159.3   0.0117  0.868   1.750  1.014   0.085
      10   0.1634   0.2154   0.857       93822.    5159.3   0.0117  0.868   1.750  1.014   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1638   0.1634
             R free    0.2159   0.2154
     Rms BondLength    0.0117   0.0117
      Rms BondAngle    1.7472   1.7504
     Rms ChirVolume    0.0852   0.0854
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.2s System:    0.1s Elapsed:     0:50