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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 04:08:40 


 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 1.46     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_1-47A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-46A.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_1-46A.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       0.1173
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4600
  Estimated number of reflections :      47040
  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  1.4600

  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_1-47A.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=   2.055 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=   2.194 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=   1.832 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=   2.218 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=   2.408 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=   2.386 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=   2.098 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       1838
Number of   all  reflections      36707
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          36707

   Current auto weighting coefficient =    6.1496744    

 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.= 0.896 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        :   144  144  288
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    89   89  188
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    89   89  188
 Weight matrix   0.26843593    
 Actual weight    6.1496744      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                82.6
Norm of X_ray B-factor gradient                  91.9
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.499
Product of X_ray and Geom B-fact gradients     -0.270E+08
 Cosine of angle between them                      -0.902


Residuals: XRAY=     0.1024E+07 GEOM=     0.1316E+05 TOTAL=     0.1037E+07
 function value    1036926.2    

-------------------------------------------------------------------------------
             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     1.844     1.644
Bond angles  : others                          3238     2.365     1.580
Torsion angles, period  1. refined              185     6.743     5.000
Torsion angles, period  2. refined               90    34.647    22.778
Torsion angles, period  3. refined              268    13.303    15.000
Torsion angles, period  4. refined                9    12.404    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   306     0.244     0.200
VDW repulsions.others                          1336     0.220     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             727     0.081     0.200
HBOND: refined_atoms                            207     0.199     0.200
HBOND.others                                      1     0.078     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 23     0.199     0.200
HBOND: symmetry: refined_atoms                   21     0.173     0.200
M. chain bond B values: refined atoms           746     1.817     1.650
M. chain bond B values: others                  746     1.811     1.650
M. chain angle B values: refined atoms          929     2.801     2.465
M. chain angle B values: others                 930     2.801     2.465
S. chain bond B values: refined atoms           811     3.256     2.066
S. chain bond B values: others                  810     3.251     2.066
S. chain angle B values: refined atoms         1177     4.950     2.927
S. chain angle B values: others                1178     4.948     2.927
Long range B values: refined atoms             1844     7.853    22.602
Long range B values: others                    1757     7.595    21.181
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0462, B  =    0.1005
Partial structure    1: scale =     0.3947, B  =   37.4971
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.059    4691 100.00   393.5   403.2  0.17  0.18     216   389.6   394.8  0.21  0.22
 0.176    7998  99.98   216.3   194.4  0.19  0.16     453   228.4   205.5  0.22  0.20
 0.293   10168 100.00   107.4   100.8  0.22  0.19     564   106.8   101.1  0.26  0.23
 0.411   12000 100.00    44.0    54.8  0.43  0.40     605    44.3    55.2  0.45  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0591   3522   0.896   1169   0.788   4691   0.869  0.945  0.9572  0.9662  0.9019  0.9356
  0.1763   6820   0.865   1178   0.764   7998   0.850  1.075  0.9458  0.9549  0.8915  0.9341
  0.2934   8989   0.818   1179   0.734  10168   0.809  0.990  0.9310  0.9405  0.8930  0.9247
  0.4106  10827   0.520   1183   0.461  12010   0.515  0.505  0.7103  0.7120  0.7130  0.7275
 $$
Resolution limits                    =     41.964     1.460
Number of used reflections           =      34865
Percentage observed                  =    99.9918
Percentage of free reflections       =     5.0078
Overall R factor                     =     0.2127
Free R factor                        =     0.2484
Average Fourier shell correlation    =     0.8685
AverageFree Fourier shell correlation=     0.8651
Overall weighted R factor            =     0.1792
Free weighted R factor               =     0.2140
Overall weighted R2 factor           =     0.2080
Free weighted R2 factor              =     0.2495
Average correlation coefficient      =     0.8605
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9402
Cruickshanks DPI for coordinate error=     0.0816
DPI based on free R factor           =     0.0847
Overall figure of merit              =     0.7250
ML based su of positional parameters =     0.0734
ML based su of thermal parameters    =     2.1064
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    166474.88       13159.957       1036926.2      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35080063    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1023742.7    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =   -0.0591
Partial structure    1: scale =     0.3937, B  =   37.4614
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2131
Free R factor                        =     0.2477
Average Fourier shell correlation    =     0.8896
AverageFree Fourier shell correlation=     0.8860
Average correlation coefficient      =     0.8588
Overall figure of merit              =     0.7647
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    165144.98       8154.8389       1023742.7       1036926.2    


     CGMAT cycle number =      3

 Weight matrix   0.35703152    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1023059.0    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =   -0.0058
Partial structure    1: scale =     0.3944, B  =   37.6721
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2125
Free R factor                        =     0.2474
Average Fourier shell correlation    =     0.8923
AverageFree Fourier shell correlation=     0.8883
Average correlation coefficient      =     0.8599
Overall figure of merit              =     0.7678
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    164966.53       8568.5684       1023059.0       1023742.7    


     CGMAT cycle number =      4

 Weight matrix   0.35766539    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1022997.6    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =    0.0051
Partial structure    1: scale =     0.3946, B  =   37.6210
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2124
Free R factor                        =     0.2475
Average Fourier shell correlation    =     0.8928
AverageFree Fourier shell correlation=     0.8886
Average correlation coefficient      =     0.8604
Overall figure of merit              =     0.7684
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    164941.84       8658.9629       1022997.6       1023059.0    


     CGMAT cycle number =      5

 Weight matrix   0.35744274    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1023009.6    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =    0.0109
Partial structure    1: scale =     0.3945, B  =   37.5784
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2124
Free R factor                        =     0.2475
Average Fourier shell correlation    =     0.8929
AverageFree Fourier shell correlation=     0.8886
Average correlation coefficient      =     0.8606
Overall figure of merit              =     0.7684
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    164936.08       8692.0020       1022995.2       1022997.6    


     CGMAT cycle number =      6

 Weight matrix   0.35750979    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1023006.4    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =    0.0089
Partial structure    1: scale =     0.3946, B  =   37.5944
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2124
Free R factor                        =     0.2476
Average Fourier shell correlation    =     0.8929
AverageFree Fourier shell correlation=     0.8886
Average correlation coefficient      =     0.8607
Overall figure of merit              =     0.7685
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    164935.88       8699.7314       1023048.0       1022995.2    

 fvalues    164935.88       8699.7314       1023015.0       1023001.7    
 fvalues    164935.88       8699.7314       1023015.0       1023001.7    


     CGMAT cycle number =      7

 Weight matrix   0.35809258    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1022986.2    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =    0.0001
Partial structure    1: scale =     0.3946, B  =   37.5999
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2124
Free R factor                        =     0.2476
Average Fourier shell correlation    =     0.8930
AverageFree Fourier shell correlation=     0.8887
Average correlation coefficient      =     0.8607
Overall figure of merit              =     0.7686
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    164933.45       8699.1250       1022986.2       1023001.7    


     CGMAT cycle number =      8

 Weight matrix   0.35694957    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1023034.3    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =    0.0124
Partial structure    1: scale =     0.3945, B  =   37.5031
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2124
Free R factor                        =     0.2476
Average Fourier shell correlation    =     0.8928
AverageFree Fourier shell correlation=     0.8885
Average correlation coefficient      =     0.8607
Overall figure of merit              =     0.7683
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    164938.44       8695.5352       1023032.8       1022986.2    

 fvalues    164938.44       8695.5352       1023035.8       1023013.3    
 fvalues    164938.44       8695.5352       1023035.8       1023013.3    


     CGMAT cycle number =      9

 Weight matrix   0.35727197    
 Actual weight    6.1496744      is applied to the X-ray term


 function value    1023015.1    

-------------------------------------------------------------------------------
             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 =     0.0461, B  =    0.0088
Partial structure    1: scale =     0.3945, B  =   37.5045
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2124
Free R factor                        =     0.2476
Average Fourier shell correlation    =     0.8929
AverageFree Fourier shell correlation=     0.8885
Average correlation coefficient      =     0.8607
Overall figure of merit              =     0.7684
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    164944.67       8695.1973       1023028.9       1023013.3    
 fvalues    164944.67       8695.1973       1023028.9       1023051.2    


     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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    89   89  188
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    89   89  188
 Weight matrix   0.35698715    
 Actual weight    6.1496744      is applied to the X-ray term
Norm of X_ray positional gradient                43.7
Norm of Geom. positional gradient                43.8
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.185E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.363E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.1014E+07 GEOM=      8695.     TOTAL=     0.1023E+07
 function value    1023041.3    

-------------------------------------------------------------------------------
             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     1.848     1.644
Bond angles  : others                          3238     1.513     1.580
Torsion angles, period  1. refined              185     6.730     5.000
Torsion angles, period  2. refined               90    34.659    22.778
Torsion angles, period  3. refined              268    13.320    15.000
Torsion angles, period  4. refined                9    12.444    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.244     0.200
VDW repulsions.others                          1366     0.194     0.200
VDW; torsion: refined_atoms                     731     0.173     0.200
VDW; torsion.others                             762     0.085     0.200
HBOND: refined_atoms                            205     0.200     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.164     0.200
M. chain bond B values: refined atoms           746     1.836     1.659
M. chain bond B values: others                  746     1.831     1.659
M. chain angle B values: refined atoms          929     2.822     2.479
M. chain angle B values: others                 930     2.821     2.479
S. chain bond B values: refined atoms           811     3.267     2.077
S. chain bond B values: others                  810     3.262     2.076
S. chain angle B values: refined atoms         1177     4.970     2.942
S. chain angle B values: others                1178     4.968     2.941
Long range B values: refined atoms             1842     7.726    22.675
Long range B values: others                    1756     7.447    21.256
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0461, B  =    0.0110
Partial structure    1: scale =     0.3945, B  =   37.4994
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.059    4691 100.00   394.0   403.6  0.17  0.18     216   390.1   395.4  0.21  0.22
 0.176    7998  99.98   216.6   194.6  0.19  0.16     453   228.7   205.7  0.22  0.20
 0.293   10168 100.00   107.5   101.0  0.22  0.19     564   106.9   101.3  0.25  0.22
 0.411   12000 100.00    44.0    54.9  0.43  0.40     605    44.3    55.3  0.44  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0591   3522   0.913   1169   0.812   4691   0.888  0.948  0.9617  0.9703  0.9022  0.9356
  0.1763   6820   0.880   1178   0.779   7998   0.865  1.077  0.9490  0.9584  0.8924  0.9339
  0.2934   8989   0.842   1179   0.760  10168   0.833  0.996  0.9393  0.9485  0.8940  0.9259
  0.4106  10827   0.608   1183   0.550  12010   0.603  0.551  0.7697  0.7717  0.7134  0.7274
 $$
Resolution limits                    =     41.964     1.460
Number of used reflections           =      34865
Percentage observed                  =    99.9918
Percentage of free reflections       =     5.0078
Overall R factor                     =     0.2124
Free R factor                        =     0.2477
Average Fourier shell correlation    =     0.8928
AverageFree Fourier shell correlation=     0.8885
Overall weighted R factor            =     0.1792
Free weighted R factor               =     0.2138
Overall weighted R2 factor           =     0.2081
Free weighted R2 factor              =     0.2497
Average correlation coefficient      =     0.8607
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9404
Cruickshanks DPI for coordinate error=     0.0815
DPI based on free R factor           =     0.0844
Overall figure of merit              =     0.7683
ML based su of positional parameters =     0.0635
ML based su of thermal parameters    =     1.8075
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    164943.09       8694.9102       1023041.3       1023051.2    

    ****                              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.= 0.913 id.= 3.000 dev= -2.09 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_1-46A.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     1.848     1.644
Bond angles  : others                          3238     1.513     1.580
Torsion angles, period  1. refined              185     6.729     5.000
Torsion angles, period  2. refined               90    34.658    22.778
Torsion angles, period  3. refined              268    13.321    15.000
Torsion angles, period  4. refined                9    12.444    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   306     0.244     0.200
VDW repulsions.others                          1365     0.194     0.200
VDW; torsion: refined_atoms                     731     0.173     0.200
VDW; torsion.others                             762     0.085     0.200
HBOND: refined_atoms                            205     0.200     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.164     0.200
M. chain bond B values: refined atoms           746     1.836     1.659
M. chain bond B values: others                  746     1.831     1.659
M. chain angle B values: refined atoms          929     2.822     2.479
M. chain angle B values: others                 930     2.821     2.479
S. chain bond B values: refined atoms           811     3.267     2.077
S. chain bond B values: others                  810     3.262     2.076
S. chain angle B values: refined atoms         1177     4.970     2.942
S. chain angle B values: others                1178     4.968     2.941
Long range B values: refined atoms             1843     7.729    22.691
Long range B values: others                    1757     7.450    21.273
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0461, B  =    0.0119
Partial structure    1: scale =     0.3944, B  =   37.5027
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.059    4691 100.00   394.0   403.6  0.17  0.18     216   390.1   395.4  0.21  0.22
 0.176    7998  99.98   216.6   194.6  0.19  0.16     453   228.7   205.7  0.22  0.20
 0.293   10168 100.00   107.5   101.0  0.22  0.19     564   106.9   101.3  0.25  0.22
 0.411   12000 100.00    44.0    54.9  0.43  0.40     605    44.3    55.3  0.44  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0591   3522   0.913   1169   0.812   4691   0.888  0.948  0.9617  0.9703  0.9022  0.9356
  0.1763   6820   0.880   1178   0.779   7998   0.865  1.077  0.9490  0.9584  0.8924  0.9339
  0.2934   8989   0.842   1179   0.760  10168   0.833  0.996  0.9393  0.9485  0.8940  0.9258
  0.4106  10827   0.608   1183   0.550  12010   0.603  0.551  0.7696  0.7717  0.7134  0.7274
 $$
Resolution limits                    =     41.964     1.460
Number of used reflections           =      34865
Percentage observed                  =    99.9918
Percentage of free reflections       =     5.0078
Overall R factor                     =     0.2124
Free R factor                        =     0.2477
Average Fourier shell correlation    =     0.8928
AverageFree Fourier shell correlation=     0.8885
Overall weighted R factor            =     0.1792
Free weighted R factor               =     0.2138
Overall weighted R2 factor           =     0.2081
Free weighted R2 factor              =     0.2498
Average correlation coefficient      =     0.8607
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9404
Cruickshanks DPI for coordinate error=     0.0815
DPI based on free R factor           =     0.0844
Overall figure of merit              =     0.7683
ML based su of positional parameters =     0.0635
ML based su of thermal parameters    =     1.8075
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.57
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2127   0.2484   0.725      166475.    8960.4   0.0130  0.983   1.844  1.073   0.090
       1   0.2131   0.2477   0.765      165145.    8916.6   0.0119  0.895   1.776  1.033   0.087
       2   0.2125   0.2474   0.768      164967.    8912.2   0.0130  0.979   1.821  1.060   0.090
       3   0.2124   0.2475   0.768      164942.    8912.3   0.0131  0.987   1.837  1.070   0.090
       4   0.2124   0.2475   0.768      164938.    8912.5   0.0131  0.991   1.843  1.074   0.090
       5   0.2124   0.2476   0.768      164937.    8912.8   0.0132  0.992   1.847  1.075   0.090
       6   0.2124   0.2476   0.769      164933.    8912.9   0.0132  0.992   1.847  1.076   0.091
       7   0.2124   0.2476   0.768      164942.    8913.3   0.0132  0.992   1.848  1.076   0.091
       8   0.2124   0.2476   0.768      164939.    8913.2   0.0132  0.992   1.848  1.076   0.091
       9   0.2124   0.2477   0.768      164943.    8913.4   0.0132  0.992   1.848  1.076   0.091
      10   0.2124   0.2477   0.768      164944.    8913.5   0.0132  0.992   1.848  1.076   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2127   0.2124
             R free    0.2484   0.2477
     Rms BondLength    0.0130   0.0132
      Rms BondAngle    1.8441   1.8483
     Rms ChirVolume    0.0904   0.0906
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.6s System:    0.2s Elapsed:     1:02