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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:01:54 


 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 1.70     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_1-71A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-70A.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_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  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  1.7000

  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_1-71A.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=   2.045 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.202 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.827 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=   2.226 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=   2.411 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=   2.402 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=   2.116 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       1202
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 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.= 0.890 id.= 3.000 dev= -2.11 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                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.29219300    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                80.9
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.470
Product of X_ray and Geom B-fact gradients     -0.396E+08
 Cosine of angle between them                      -0.917


Residuals: XRAY=     0.7814E+06 GEOM=     0.1354E+05 TOTAL=     0.7950E+06
 function value    794977.00    

-------------------------------------------------------------------------------
             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     1.817     1.644
Bond angles  : others                          3238     2.357     1.580
Torsion angles, period  1. refined              185     6.845     5.000
Torsion angles, period  2. refined               90    35.285    22.778
Torsion angles, period  3. refined              268    13.406    15.000
Torsion angles, period  4. refined                9    12.097    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   292     0.248     0.200
VDW repulsions.others                          1336     0.219     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             724     0.080     0.200
HBOND: refined_atoms                            211     0.200     0.200
HBOND.others                                      2     0.065     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 24     0.189     0.200
HBOND: symmetry: refined_atoms                   24     0.173     0.200
M. chain bond B values: refined atoms           746     1.682     1.383
M. chain bond B values: others                  746     1.679     1.383
M. chain angle B values: refined atoms          929     2.644     2.062
M. chain angle B values: others                 930     2.642     2.062
S. chain bond B values: refined atoms           811     3.032     1.782
S. chain bond B values: others                  810     3.025     1.781
S. chain angle B values: refined atoms         1177     4.670     2.505
S. chain angle B values: others                1178     4.668     2.504
Long range B values: refined atoms             1829     7.083    19.094
Long range B values: others                    1739     6.768    17.669
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    0.0668
Partial structure    1: scale =     0.3865, B  =   43.8942
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   453.4   462.4  0.16  0.17     135   451.9   463.5  0.20  0.21
 0.130    5109 100.00   298.4   285.4  0.16  0.15     291   304.5   283.5  0.22  0.19
 0.216    6518  99.97   201.9   185.7  0.17  0.14     354   207.4   193.0  0.20  0.17
 0.303    7621 100.00   104.2   116.1  0.25  0.19     422   102.2   114.8  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.911    857   0.815   3036   0.884  0.950  0.9615  0.9701  0.9005  0.9397
  0.1301   4247   0.870    862   0.763   5109   0.852  0.998  0.9463  0.9586  0.8963  0.9425
  0.2165   5641   0.885    877   0.777   6518   0.870  1.047  0.9555  0.9620  0.9131  0.9424
  0.3028   6772   0.766    852   0.695   7624   0.758  0.824  0.9099  0.9221  0.8606  0.9052
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1778
Free R factor                        =     0.2235
Average Fourier shell correlation    =     0.9487
AverageFree Fourier shell correlation=     0.9379
Overall weighted R factor            =     0.1589
Free weighted R factor               =     0.1977
Overall weighted R2 factor           =     0.1907
Free weighted R2 factor              =     0.2337
Average correlation coefficient      =     0.9293
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9319
Cruickshanks DPI for coordinate error=     0.1078
DPI based on free R factor           =     0.1110
Overall figure of merit              =     0.8294
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.2777
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115773.45       13542.441       794977.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34855780    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785334.38    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0677
Partial structure    1: scale =     0.3863, B  =   44.1008
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2232
Average Fourier shell correlation    =     0.9543
AverageFree Fourier shell correlation=     0.9440
Average correlation coefficient      =     0.9290
Overall figure of merit              =     0.8537
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115061.30       8706.5781       785334.38       794977.00    


     CGMAT cycle number =      3

 Weight matrix   0.35335970    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784792.38    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0404
Partial structure    1: scale =     0.3862, B  =   43.8689
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1775
Free R factor                        =     0.2230
Average Fourier shell correlation    =     0.9549
AverageFree Fourier shell correlation=     0.9445
Average correlation coefficient      =     0.9299
Overall figure of merit              =     0.8551
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114933.67       9026.0527       784792.38       785334.38    


     CGMAT cycle number =      4

 Weight matrix   0.35447863    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784654.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0247
Partial structure    1: scale =     0.3863, B  =   43.7573
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1774
Free R factor                        =     0.2229
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9447
Average correlation coefficient      =     0.9300
Overall figure of merit              =     0.8554
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114898.58       9124.7969       784654.25       784792.38    


     CGMAT cycle number =      5

 Weight matrix   0.35488886    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784581.69    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0195
Partial structure    1: scale =     0.3864, B  =   43.6645
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                     =     0.1774
Free R factor                        =     0.2227
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9447
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8556
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114882.70       9159.4404       784581.69       784654.25    


     CGMAT cycle number =      6

 Weight matrix   0.35504150    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784554.94    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0192
Partial structure    1: scale =     0.3866, B  =   43.6499
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                     =     0.1774
Free R factor                        =     0.2227
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8557
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114876.72       9172.9834       784554.94       784581.69    


     CGMAT cycle number =      7

 Weight matrix   0.35483986    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784553.81    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0160
Partial structure    1: scale =     0.3866, B  =   43.6040
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                     =     0.1775
Free R factor                        =     0.2228
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8556
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114876.09       9176.2168       784553.81       784554.94    


     CGMAT cycle number =      8

 Weight matrix   0.35471132    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784567.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0186
Partial structure    1: scale =     0.3867, B  =   43.6651
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                     =     0.1775
Free R factor                        =     0.2228
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8556
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114877.73       9176.1836       784560.44       784553.81    
 fvalues    114877.73       9176.1836       784560.44       784564.94    


     CGMAT cycle number =      9

 Weight matrix   0.35358229    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784577.75    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0002
Partial structure    1: scale =     0.3867, B  =   43.6675
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                     =     0.1776
Free R factor                        =     0.2228
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9447
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8555
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    114880.97       9167.0410       784544.19       784564.94    
 fvalues    114880.97       9167.0410       784544.19       784577.69    


     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.= 0.914 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.35461944    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.7
Norm of Geom. positional gradient                41.7
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                  128.
Product of X_ray and Geom posit. gradients     -0.168E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.521E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7754E+06 GEOM=      9163.     TOTAL=     0.7845E+06
 function value    784538.06    

-------------------------------------------------------------------------------
             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     1.836     1.644
Bond angles  : others                          3238     1.514     1.580
Torsion angles, period  1. refined              185     6.825     5.000
Torsion angles, period  2. refined               90    35.213    22.778
Torsion angles, period  3. refined              268    13.555    15.000
Torsion angles, period  4. refined                9    12.295    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   294     0.248     0.200
VDW repulsions.others                          1370     0.191     0.200
VDW; torsion: refined_atoms                     721     0.174     0.200
VDW; torsion.others                             781     0.085     0.200
HBOND: refined_atoms                            202     0.206     0.200
HBOND.others                                      1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 23     0.179     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     1.703     1.391
M. chain angle B values: refined atoms          929     2.671     2.074
M. chain angle B values: others                 930     2.669     2.074
S. chain bond B values: refined atoms           811     3.056     1.794
S. chain bond B values: others                  810     3.049     1.793
S. chain angle B values: refined atoms         1177     4.706     2.521
S. chain angle B values: others                1178     4.704     2.521
Long range B values: refined atoms             1819     7.034    19.150
Long range B values: others                    1733     6.765    17.801
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0187
Partial structure    1: scale =     0.3868, B  =   43.6807
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   453.6   462.9  0.16  0.17     135   452.0   462.9  0.21  0.21
 0.130    5109 100.00   298.5   285.3  0.17  0.15     291   304.6   283.5  0.21  0.19
 0.216    6518  99.97   202.0   185.8  0.17  0.14     354   207.4   192.6  0.20  0.17
 0.303    7621 100.00   104.3   116.0  0.25  0.19     422   102.2   114.8  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.926    857   0.833   3036   0.900  0.952  0.9647  0.9731  0.9003  0.9401
  0.1301   4247   0.872    862   0.765   5109   0.854  0.998  0.9474  0.9590  0.8980  0.9419
  0.2165   5641   0.891    877   0.783   6518   0.876  1.047  0.9576  0.9637  0.9145  0.9423
  0.3028   6772   0.830    852   0.754   7624   0.821  0.843  0.9259  0.9378  0.8627  0.9078
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1776
Free R factor                        =     0.2227
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9448
Overall weighted R factor            =     0.1590
Free weighted R factor               =     0.1972
Overall weighted R2 factor           =     0.1908
Free weighted R2 factor              =     0.2331
Average correlation coefficient      =     0.9301
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9324
Cruickshanks DPI for coordinate error=     0.1077
DPI based on free R factor           =     0.1106
Overall figure of merit              =     0.8556
ML based su of positional parameters =     0.0668
ML based su of thermal parameters    =     2.0206
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114875.73       9162.7979       784538.06       784577.69    

    ****                              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= -2.09 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_1-70A.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     1.513     1.580
Torsion angles, period  1. refined              185     6.825     5.000
Torsion angles, period  2. refined               90    35.214    22.778
Torsion angles, period  3. refined              268    13.569    15.000
Torsion angles, period  4. refined                9    12.297    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   294     0.248     0.200
VDW repulsions.others                          1370     0.191     0.200
VDW; torsion: refined_atoms                     720     0.174     0.200
VDW; torsion.others                             787     0.084     0.200
HBOND: refined_atoms                            204     0.205     0.200
HBOND.others                                      1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 23     0.179     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             1820     7.046    19.159
Long range B values: others                    1734     6.779    17.810
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0177
Partial structure    1: scale =     0.3868, B  =   43.7624
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   453.6   462.9  0.16  0.17     135   452.0   462.9  0.21  0.21
 0.130    5109 100.00   298.5   285.3  0.17  0.15     291   304.6   283.5  0.21  0.19
 0.216    6518  99.97   202.0   185.8  0.17  0.14     354   207.4   192.6  0.20  0.17
 0.303    7621 100.00   104.3   116.0  0.25  0.19     422   102.2   114.8  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.926    857   0.833   3036   0.900  0.952  0.9647  0.9731  0.9002  0.9401
  0.1301   4247   0.872    862   0.765   5109   0.854  0.998  0.9474  0.9590  0.8979  0.9419
  0.2165   5641   0.891    877   0.783   6518   0.876  1.047  0.9575  0.9637  0.9145  0.9423
  0.3028   6772   0.830    852   0.754   7624   0.821  0.843  0.9259  0.9378  0.8628  0.9078
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1776
Free R factor                        =     0.2228
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9448
Overall weighted R factor            =     0.1590
Free weighted R factor               =     0.1972
Overall weighted R2 factor           =     0.1907
Free weighted R2 factor              =     0.2331
Average correlation coefficient      =     0.9301
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9323
Cruickshanks DPI for coordinate error=     0.1077
DPI based on free R factor           =     0.1106
Overall figure of merit              =     0.8556
ML based su of positional parameters =     0.0668
ML based su of thermal parameters    =     2.0206
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.71
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1778   0.2235   0.829      115773.    6410.5   0.0128  0.960   1.817  1.055   0.090
       1   0.1779   0.2232   0.854      115061.    6390.5   0.0120  0.900   1.775  1.029   0.087
       2   0.1775   0.2230   0.855      114934.    6386.7   0.0127  0.958   1.810  1.050   0.090
       3   0.1774   0.2229   0.855      114899.    6384.9   0.0128  0.966   1.822  1.058   0.090
       4   0.1774   0.2227   0.856      114883.    6383.9   0.0129  0.969   1.828  1.062   0.091
       5   0.1774   0.2227   0.856      114877.    6383.7   0.0129  0.970   1.832  1.064   0.091
       6   0.1775   0.2228   0.856      114876.    6383.6   0.0129  0.971   1.834  1.065   0.091
       7   0.1775   0.2228   0.856      114878.    6384.0   0.0129  0.971   1.835  1.066   0.091
       8   0.1776   0.2228   0.855      114881.    6383.8   0.0129  0.971   1.836  1.066   0.091
       9   0.1776   0.2227   0.856      114876.    6383.8   0.0129  0.970   1.836  1.066   0.091
      10   0.1776   0.2228   0.856      114876.    6383.9   0.0129  0.971   1.837  1.067   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1778   0.1776
             R free    0.2235   0.2228
     Rms BondLength    0.0128   0.0129
      Rms BondAngle    1.8166   1.8367
     Rms ChirVolume    0.0900   0.0910
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.9s System:    0.7s Elapsed:     0:50