###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:20:38 


 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 1.69     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_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-69A.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_1-69A.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       0.0875
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6900
  Estimated number of reflections :      31298
  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  1.6900

  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_1-70A.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=   2.049 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=   2.204 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=   1.834 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=   2.232 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=   2.412 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=   2.393 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.128 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:22-OCT-19
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            0
Number of "free" reflections       1224
Number of   all  reflections      23909
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23909

   Current auto weighting coefficient =    6.7246294    

 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.= 0.902 id.= 3.000 dev= -2.10 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                 :    35   35   73
 Minimum acceptable grid spacing:    79   79  168
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   73
 Minimum acceptable grid spacing:    79   79  168
 Weight matrix   0.29483676    
 Actual weight    6.7246294      is applied to the X-ray term
Norm of X_ray positional gradient                37.0
Norm of Geom. positional gradient                81.4
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -0.471
Product of X_ray and Geom B-fact gradients     -0.391E+08
 Cosine of angle between them                      -0.896


Residuals: XRAY=     0.7898E+06 GEOM=     0.1368E+05 TOTAL=     0.8035E+06
 function value    803500.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.837     1.644
Bond angles  : others                          3238     2.361     1.580
Torsion angles, period  1. refined              185     6.826     5.000
Torsion angles, period  2. refined               90    35.211    22.778
Torsion angles, period  3. refined              268    13.570    15.000
Torsion angles, period  4. refined                9    12.278    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   295     0.248     0.200
VDW repulsions.others                          1324     0.220     0.200
VDW; torsion: refined_atoms                     721     0.174     0.200
VDW; torsion.others                             723     0.081     0.200
HBOND: refined_atoms                            205     0.205     0.200
HBOND.others                                      1     0.091     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 22     0.198     0.200
HBOND: symmetry: refined_atoms                   22     0.179     0.200
M. chain bond B values: refined atoms           746     1.707     1.391
M. chain bond B values: others                  746     1.704     1.391
M. chain angle B values: refined atoms          929     2.671     2.074
M. chain angle B values: others                 930     2.670     2.074
S. chain bond B values: refined atoms           811     3.058     1.794
S. chain bond B values: others                  810     3.051     1.793
S. chain angle B values: refined atoms         1177     4.708     2.522
S. chain angle B values: others                1178     4.706     2.521
Long range B values: refined atoms             1823     7.041    19.167
Long range B values: others                    1737     6.774    17.821
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0429, B  =    0.0969
Partial structure    1: scale =     0.3868, B  =   43.6845
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3097 100.00   451.0   460.7  0.16  0.17     139   442.7   454.0  0.21  0.21
 0.132    5198 100.00   294.0   280.8  0.17  0.15     299   300.4   279.1  0.22  0.19
 0.219    6626  99.97   198.2   181.6  0.17  0.15     360   204.7   189.3  0.20  0.17
 0.306    7756 100.00   100.1   112.6  0.25  0.19     426    97.1   111.2  0.32  0.24
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0443   2221   0.912    876   0.815   3097   0.885  0.950  0.9608  0.9702  0.9029  0.9400
  0.1317   4322   0.872    876   0.767   5198   0.854  1.001  0.9471  0.9586  0.8973  0.9415
  0.2190   5749   0.883    877   0.767   6626   0.868  1.049  0.9561  0.9613  0.9146  0.9422
  0.3064   6885   0.758    877   0.686   7762   0.750  0.814  0.9060  0.9187  0.8616  0.9022
 $$
Resolution limits                    =     41.964     1.690
Number of used reflections           =      22682
Percentage observed                  =    99.9874
Percentage of free reflections       =     5.1201
Overall R factor                     =     0.1793
Free R factor                        =     0.2248
Average Fourier shell correlation    =     0.9473
AverageFree Fourier shell correlation=     0.9370
Overall weighted R factor            =     0.1597
Free weighted R factor               =     0.1983
Overall weighted R2 factor           =     0.1914
Free weighted R2 factor              =     0.2343
Average correlation coefficient      =     0.9281
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9324
Cruickshanks DPI for coordinate error=     0.1067
DPI based on free R factor           =     0.1100
Overall figure of merit              =     0.8268
ML based su of positional parameters =     0.0732
ML based su of thermal parameters    =     2.2557
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    117451.82       13680.857       803500.81      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35516140    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    793512.19    

-------------------------------------------------------------------------------
             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 =     0.0428, B  =   -0.0734
Partial structure    1: scale =     0.3866, B  =   43.7890
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1794
Free R factor                        =     0.2246
Average Fourier shell correlation    =     0.9535
AverageFree Fourier shell correlation=     0.9435
Average correlation coefficient      =     0.9275
Overall figure of merit              =     0.8528
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    116702.47       8731.3262       793512.19       803500.81    


     CGMAT cycle number =      3

 Weight matrix   0.35839134    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    793083.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0188
Partial structure    1: scale =     0.3868, B  =   43.6572
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1789
Free R factor                        =     0.2245
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8542
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    116586.13       9085.0762       793083.56       793512.19    


     CGMAT cycle number =      4

 Weight matrix   0.35869947    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    792999.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0081
Partial structure    1: scale =     0.3869, B  =   43.6160
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9439
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    116559.65       9178.9932       792999.44       793083.56    


     CGMAT cycle number =      5

 Weight matrix   0.35795879    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    792988.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0009
Partial structure    1: scale =     0.3869, B  =   43.6156
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1789
Free R factor                        =     0.2243
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    116554.21       9204.6055       792988.50       792999.44    


     CGMAT cycle number =      6

 Weight matrix   0.35772571    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    792984.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0038
Partial structure    1: scale =     0.3869, B  =   43.6105
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2243
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    116552.88       9209.4434       792984.31       792988.50    


     CGMAT cycle number =      7

 Weight matrix   0.35746947    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    792990.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0073
Partial structure    1: scale =     0.3869, B  =   43.5558
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2243
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    116554.15       9205.7715       793029.06       792984.31    

 fvalues    116554.15       9205.7715       792997.38       792989.19    
 fvalues    116554.15       9205.7715       792997.38       792989.19    


     CGMAT cycle number =      8

 Weight matrix   0.35713848    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    792997.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0034
Partial structure    1: scale =     0.3869, B  =   43.5365
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2243
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8543
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    116555.83       9202.9727       793007.75       792989.19    

 fvalues    116555.83       9202.9727       792996.88       792997.75    
 fvalues    116555.83       9202.9727       792996.88       792997.75    


     CGMAT cycle number =      9

 Weight matrix   0.35688996    
 Actual weight    6.7246294      is applied to the X-ray term


 function value    793008.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0004
Partial structure    1: scale =     0.3869, B  =   43.5351
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9539
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8543
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    116557.73       9202.3232       793002.25       792997.75    
 fvalues    116557.73       9202.3232       793002.25       793009.88    


     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.= 0.915 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                 :    35   35   73
 Minimum acceptable grid spacing:    79   79  168
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   73
 Minimum acceptable grid spacing:    79   79  168
 Weight matrix   0.35727003    
 Actual weight    6.7246294      is applied to the X-ray term
Norm of X_ray positional gradient                42.3
Norm of Geom. positional gradient                42.3
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                  128.
Product of X_ray and Geom posit. gradients     -0.173E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.526E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7838E+06 GEOM=      9201.     TOTAL=     0.7930E+06
 function value    792999.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.837     1.644
Bond angles  : others                          3238     1.517     1.580
Torsion angles, period  1. refined              185     6.815     5.000
Torsion angles, period  2. refined               90    35.111    22.778
Torsion angles, period  3. refined              268    13.627    15.000
Torsion angles, period  4. refined                9    12.206    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   297     0.247     0.200
VDW repulsions.others                          1352     0.193     0.200
VDW; torsion: refined_atoms                     718     0.174     0.200
VDW; torsion.others                             764     0.085     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.019     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 23     0.183     0.200
HBOND: symmetry: refined_atoms                   21     0.179     0.200
M. chain bond B values: refined atoms           746     1.717     1.404
M. chain bond B values: others                  746     1.714     1.404
M. chain angle B values: refined atoms          929     2.678     2.094
M. chain angle B values: others                 930     2.677     2.094
S. chain bond B values: refined atoms           811     3.061     1.806
S. chain bond B values: others                  810     3.055     1.805
S. chain angle B values: refined atoms         1177     4.707     2.540
S. chain angle B values: others                1178     4.705     2.539
Long range B values: refined atoms             1837     7.127    19.416
Long range B values: others                    1747     6.876    18.039
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0085
Partial structure    1: scale =     0.3870, B  =   43.5387
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3097 100.00   451.4   461.3  0.16  0.17     139   443.2   454.7  0.21  0.21
 0.132    5198 100.00   294.3   280.8  0.17  0.15     299   300.7   279.2  0.21  0.19
 0.219    6626  99.97   198.4   181.8  0.17  0.15     360   204.9   189.1  0.20  0.17
 0.306    7756 100.00   100.2   112.7  0.25  0.19     426    97.2   111.2  0.32  0.24
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0443   2221   0.927    876   0.836   3097   0.901  0.952  0.9647  0.9733  0.9043  0.9403
  0.1317   4322   0.874    876   0.769   5198   0.856  1.001  0.9478  0.9591  0.8981  0.9419
  0.2190   5749   0.889    877   0.774   6626   0.873  1.049  0.9576  0.9629  0.9145  0.9418
  0.3064   6885   0.827    877   0.753   7762   0.818  0.833  0.9225  0.9352  0.8616  0.9040
 $$
Resolution limits                    =     41.964     1.690
Number of used reflections           =      22682
Percentage observed                  =    99.9874
Percentage of free reflections       =     5.1201
Overall R factor                     =     0.1790
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Overall weighted R factor            =     0.1596
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1911
Free weighted R2 factor              =     0.2345
Average correlation coefficient      =     0.9287
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9328
Cruickshanks DPI for coordinate error=     0.1065
DPI based on free R factor           =     0.1098
Overall figure of merit              =     0.8544
ML based su of positional parameters =     0.0664
ML based su of thermal parameters    =     2.0013
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    116556.35       9201.0752       792999.31       793009.88    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.915 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_1-69A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.837     1.644
Bond angles  : others                          3238     1.517     1.580
Torsion angles, period  1. refined              185     6.815     5.000
Torsion angles, period  2. refined               90    35.111    22.778
Torsion angles, period  3. refined              268    13.632    15.000
Torsion angles, period  4. refined                9    12.208    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   297     0.247     0.200
VDW repulsions.others                          1353     0.193     0.200
VDW; torsion: refined_atoms                     717     0.175     0.200
VDW; torsion.others                             766     0.085     0.200
HBOND: refined_atoms                            214     0.202     0.200
HBOND.others                                      1     0.019     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 23     0.183     0.200
HBOND: symmetry: refined_atoms                   21     0.179     0.200
M. chain bond B values: refined atoms           746     1.717     1.404
M. chain bond B values: others                  746     1.714     1.404
M. chain angle B values: refined atoms          929     2.678     2.094
M. chain angle B values: others                 930     2.677     2.094
S. chain bond B values: refined atoms           811     3.061     1.806
S. chain bond B values: others                  810     3.055     1.805
S. chain angle B values: refined atoms         1177     4.707     2.540
S. chain angle B values: others                1178     4.705     2.539
Long range B values: refined atoms             1838     7.151    19.437
Long range B values: others                    1747     6.877    18.040
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0428, B  =   -0.0067
Partial structure    1: scale =     0.3870, B  =   43.5477
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3097 100.00   451.4   461.3  0.16  0.17     139   443.2   454.7  0.21  0.21
 0.132    5198 100.00   294.3   280.8  0.17  0.15     299   300.7   279.2  0.21  0.19
 0.219    6626  99.97   198.4   181.8  0.17  0.15     360   204.9   189.1  0.20  0.17
 0.306    7756 100.00   100.2   112.7  0.25  0.19     426    97.1   111.2  0.32  0.24
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0443   2221   0.927    876   0.836   3097   0.901  0.952  0.9647  0.9733  0.9043  0.9404
  0.1317   4322   0.874    876   0.769   5198   0.856  1.001  0.9478  0.9591  0.8981  0.9419
  0.2190   5749   0.889    877   0.774   6626   0.873  1.049  0.9576  0.9629  0.9145  0.9418
  0.3064   6885   0.826    877   0.753   7762   0.818  0.833  0.9225  0.9352  0.8617  0.9040
 $$
Resolution limits                    =     41.964     1.690
Number of used reflections           =      22682
Percentage observed                  =    99.9874
Percentage of free reflections       =     5.1201
Overall R factor                     =     0.1790
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9438
Overall weighted R factor            =     0.1596
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1910
Free weighted R2 factor              =     0.2345
Average correlation coefficient      =     0.9287
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9328
Cruickshanks DPI for coordinate error=     0.1065
DPI based on free R factor           =     0.1098
Overall figure of merit              =     0.8543
ML based su of positional parameters =     0.0664
ML based su of thermal parameters    =     2.0013
-----------------------------------------------------------------------------
  Time in seconds: CPU =        18.75
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1793   0.2248   0.827      117452.    6500.3   0.0129  0.972   1.837  1.067   0.091
       1   0.1794   0.2246   0.853      116702.    6478.9   0.0120  0.906   1.781  1.034   0.088
       2   0.1789   0.2245   0.854      116586.    6477.0   0.0129  0.972   1.815  1.057   0.090
       3   0.1790   0.2244   0.854      116560.    6476.6   0.0130  0.980   1.827  1.065   0.090
       4   0.1789   0.2243   0.854      116554.    6476.6   0.0131  0.982   1.833  1.068   0.090
       5   0.1790   0.2243   0.854      116553.    6476.9   0.0131  0.982   1.836  1.070   0.090
       6   0.1790   0.2243   0.854      116554.    6477.1   0.0131  0.983   1.837  1.071   0.090
       7   0.1790   0.2243   0.854      116556.    6477.1   0.0131  0.983   1.837  1.071   0.090
       8   0.1790   0.2244   0.854      116558.    6477.2   0.0131  0.982   1.837  1.071   0.090
       9   0.1790   0.2244   0.854      116556.    6477.4   0.0131  0.982   1.837  1.071   0.090
      10   0.1790   0.2244   0.854      116557.    6477.4   0.0131  0.982   1.837  1.071   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1793   0.1790
             R free    0.2248   0.2244
     Rms BondLength    0.0129   0.0131
      Rms BondAngle    1.8370   1.8374
     Rms ChirVolume    0.0907   0.0904
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.9s System:    0.2s Elapsed:     0:52