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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: 17:08:57 


 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 1.73     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_1-74A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-73A.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_1-73A.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       0.0835
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7300
  Estimated number of reflections :      28726
  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  1.7300

  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_1-74A.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=   2.043 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.204 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.828 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=   2.223 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=   2.406 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=   2.404 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=   2.103 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       1139
Number of   all  reflections      22330
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          22330

   Current auto weighting coefficient =    6.8245711    

 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.= 0.889 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   71
 Minimum acceptable grid spacing:    78   78  165
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   71
 Minimum acceptable grid spacing:    78   78  165
 Weight matrix   0.28922278    
 Actual weight    6.8245711      is applied to the X-ray term
Norm of X_ray positional gradient                36.8
Norm of Geom. positional gradient                80.7
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  119.
Product of X_ray and Geom posit. gradients     -0.132E+08
 Cosine of angle between them                      -0.459
Product of X_ray and Geom B-fact gradients     -0.405E+08
 Cosine of angle between them                      -0.930


Residuals: XRAY=     0.7571E+06 GEOM=     0.1346E+05 TOTAL=     0.7705E+06
 function value    770539.63    

-------------------------------------------------------------------------------
             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     1.813     1.644
Bond angles  : others                          3238     2.359     1.580
Torsion angles, period  1. refined              185     6.847     5.000
Torsion angles, period  2. refined               90    35.469    22.778
Torsion angles, period  3. refined              268    13.352    15.000
Torsion angles, period  4. refined                9    12.264    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   288     0.250     0.200
VDW repulsions.others                          1327     0.220     0.200
VDW; torsion: refined_atoms                     716     0.173     0.200
VDW; torsion.others                             717     0.081     0.200
HBOND: refined_atoms                            208     0.203     0.200
HBOND.others                                      1     0.075     0.200
VDW repulsions: symmetry: refined_atoms           8     0.208     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.659     1.349
M. chain bond B values: others                  746     1.656     1.349
M. chain angle B values: refined atoms          929     2.620     2.011
M. chain angle B values: others                 930     2.619     2.011
S. chain bond B values: refined atoms           811     2.957     1.739
S. chain bond B values: others                  810     2.950     1.739
S. chain angle B values: refined atoms         1177     4.571     2.444
S. chain angle B values: others                1178     4.569     2.444
Long range B values: refined atoms             1821     7.011    18.641
Long range B values: others                    1732     6.702    17.231
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0422, B  =    0.0638
Partial structure    1: scale =     0.3849, B  =   43.6440
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.042    2898 100.00   460.8   469.5  0.16  0.17     130   454.6   465.2  0.20  0.21
 0.126    4865 100.00   309.4   296.0  0.16  0.15     277   312.5   292.0  0.22  0.20
 0.209    6167  99.97   209.3   194.8  0.17  0.14     336   217.0   203.4  0.20  0.17
 0.292    7250 100.00   117.2   127.2  0.23  0.17     396   116.4   126.5  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0423   2066   0.914    832   0.817   2898   0.886  0.951  0.9635  0.9708  0.9097  0.9404
  0.1257   4028   0.871    837   0.764   4865   0.853  0.995  0.9455  0.9589  0.8928  0.9429
  0.2090   5327   0.887    840   0.778   6167   0.872  1.038  0.9555  0.9622  0.9099  0.9402
  0.2924   6416   0.787    843   0.714   7259   0.779  0.851  0.9223  0.9330  0.8710  0.9146
 $$
Resolution limits                    =     41.964     1.730
Number of used reflections           =      21189
Percentage observed                  =    99.9866
Percentage of free reflections       =     5.1012
Overall R factor                     =     0.1742
Free R factor                        =     0.2202
Average Fourier shell correlation    =     0.9526
AverageFree Fourier shell correlation=     0.9424
Overall weighted R factor            =     0.1568
Free weighted R factor               =     0.1963
Overall weighted R2 factor           =     0.1888
Free weighted R2 factor              =     0.2311
Average correlation coefficient      =     0.9321
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9307
Cruickshanks DPI for coordinate error=     0.1117
DPI based on free R factor           =     0.1141
Overall figure of merit              =     0.8376
ML based su of positional parameters =     0.0745
ML based su of thermal parameters    =     2.3294
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    110934.02       13462.486       770539.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32919770    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    762219.69    

-------------------------------------------------------------------------------
             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 =     0.0422, B  =   -0.0699
Partial structure    1: scale =     0.3849, B  =   44.0190
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1743
Free R factor                        =     0.2200
Average Fourier shell correlation    =     0.9564
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9318
Overall figure of merit              =     0.8539
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    110408.80       8727.0273       762219.69       770539.63    


     CGMAT cycle number =      3

 Weight matrix   0.33087426    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    761966.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0422, B  =   -0.0536
Partial structure    1: scale =     0.3850, B  =   43.8032
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1739
Free R factor                        =     0.2200
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9323
Overall figure of merit              =     0.8547
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    110338.52       8953.7188       761966.88       762219.69    


     CGMAT cycle number =      4

 Weight matrix   0.33061782    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    761950.25    

-------------------------------------------------------------------------------
             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 =     0.0422, B  =   -0.0447
Partial structure    1: scale =     0.3852, B  =   43.6142
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1739
Free R factor                        =     0.2201
Average Fourier shell correlation    =     0.9567
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9323
Overall figure of merit              =     0.8547
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    110327.83       9010.1465       761950.25       761966.88    


     CGMAT cycle number =      5

 Weight matrix   0.32992381    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    761998.75    

-------------------------------------------------------------------------------
             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 =     0.0422, B  =   -0.0411
Partial structure    1: scale =     0.3852, B  =   43.5466
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1740
Free R factor                        =     0.2202
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9323
Overall figure of merit              =     0.8546
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    110332.70       9023.5615       761995.31       761950.25    
 fvalues    110332.70       9023.5615       761995.31       761996.94    


     CGMAT cycle number =      6

 Weight matrix   0.32995176    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    761980.75    

-------------------------------------------------------------------------------
             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 =     0.0422, B  =   -0.0443
Partial structure    1: scale =     0.3854, B  =   43.5031
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1740
Free R factor                        =     0.2203
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9323
Overall figure of merit              =     0.8546
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    110330.43       9022.8574       761980.75       761996.94    


     CGMAT cycle number =      7

 Weight matrix   0.32935765    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    762019.94    

-------------------------------------------------------------------------------
             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 =     0.0422, B  =   -0.0474
Partial structure    1: scale =     0.3855, B  =   43.5355
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1740
Free R factor                        =     0.2204
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9323
Overall figure of merit              =     0.8545
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    110337.16       9017.2617       762063.75       761980.75    

 fvalues    110337.16       9017.2617       762029.38       762021.00    
 fvalues    110337.16       9017.2617       762029.38       762021.00    


     CGMAT cycle number =      8

 Weight matrix   0.32929793    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    762021.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0422, B  =   -0.0482
Partial structure    1: scale =     0.3855, B  =   43.5184
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1740
Free R factor                        =     0.2204
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9322
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02

 fvalues    110337.59       9013.8848       762020.56       762021.00    


     CGMAT cycle number =      9

 Weight matrix   0.32919231    
 Actual weight    6.8245711      is applied to the X-ray term


 function value    762023.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0422, B  =   -0.0470
Partial structure    1: scale =     0.3854, B  =   43.5465
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1740
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9322
Overall figure of merit              =     0.8544
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    110338.19       9012.4395       762036.81       762020.56    

 fvalues    110338.19       9012.4395       762042.06       762023.25    
 fvalues    110338.19       9012.4395       762042.06       762023.25    


     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.= 0.906 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   71
 Minimum acceptable grid spacing:    78   78  165
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   71
 Minimum acceptable grid spacing:    78   78  165
 Weight matrix   0.32917368    
 Actual weight    6.8245711      is applied to the X-ray term
Norm of X_ray positional gradient                40.0
Norm of Geom. positional gradient                40.0
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                  125.
Product of X_ray and Geom posit. gradients     -0.155E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.487E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.7530E+06 GEOM=      9012.     TOTAL=     0.7620E+06
 function value    762027.63    

-------------------------------------------------------------------------------
             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     1.817     1.644
Bond angles  : others                          3238     1.497     1.580
Torsion angles, period  1. refined              185     6.850     5.000
Torsion angles, period  2. refined               90    35.297    22.778
Torsion angles, period  3. refined              268    13.369    15.000
Torsion angles, period  4. refined                9    12.306    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   291     0.249     0.200
VDW repulsions.others                          1353     0.194     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             767     0.084     0.200
HBOND: refined_atoms                            218     0.198     0.200
HBOND.others                                      1     0.009     0.200
VDW repulsions: symmetry: refined_atoms           8     0.214     0.200
VDW repulsions: symmetry: others                 22     0.186     0.200
HBOND: symmetry: refined_atoms                   22     0.180     0.200
M. chain bond B values: refined atoms           746     1.675     1.363
M. chain bond B values: others                  746     1.672     1.363
M. chain angle B values: refined atoms          929     2.635     2.032
M. chain angle B values: others                 930     2.633     2.032
S. chain bond B values: refined atoms           811     2.989     1.758
S. chain bond B values: others                  810     2.982     1.757
S. chain angle B values: refined atoms         1177     4.615     2.470
S. chain angle B values: others                1178     4.613     2.470
Long range B values: refined atoms             1837     7.107    18.916
Long range B values: others                    1747     6.798    17.520
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0422, B  =   -0.0469
Partial structure    1: scale =     0.3854, B  =   43.5529
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.042    2898 100.00   461.3   469.9  0.16  0.17     130   455.0   466.3  0.20  0.21
 0.126    4865 100.00   309.7   296.1  0.17  0.15     277   312.8   292.1  0.22  0.20
 0.209    6167  99.97   209.5   195.0  0.16  0.14     336   217.2   203.5  0.20  0.17
 0.292    7250 100.00   117.4   127.4  0.23  0.17     396   116.5   126.5  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0423   2066   0.929    832   0.836   2898   0.902  0.954  0.9669  0.9739  0.9097  0.9413
  0.1257   4028   0.871    837   0.763   4865   0.853  0.995  0.9457  0.9586  0.8929  0.9410
  0.2090   5327   0.890    840   0.783   6167   0.876  1.038  0.9562  0.9636  0.9096  0.9421
  0.2924   6416   0.827    843   0.751   7259   0.818  0.862  0.9318  0.9422  0.8711  0.9143
 $$
Resolution limits                    =     41.964     1.730
Number of used reflections           =      21189
Percentage observed                  =    99.9866
Percentage of free reflections       =     5.1012
Overall R factor                     =     0.1740
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9464
Overall weighted R factor            =     0.1566
Free weighted R factor               =     0.1964
Overall weighted R2 factor           =     0.1885
Free weighted R2 factor              =     0.2314
Average correlation coefficient      =     0.9322
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9306
Cruickshanks DPI for coordinate error=     0.1116
DPI based on free R factor           =     0.1142
Overall figure of merit              =     0.8544
ML based su of positional parameters =     0.0697
ML based su of thermal parameters    =     2.1511
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    110338.85       9012.0781       762049.38       762023.25    

 fvalues    110338.85       9012.0781       762031.50       762027.38    
 fvalues    110338.85       9012.0781       762031.50       762027.38    

    ****                              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.= 0.906 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_1-73A.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     1.817     1.644
Bond angles  : others                          3238     1.497     1.580
Torsion angles, period  1. refined              185     6.850     5.000
Torsion angles, period  2. refined               90    35.296    22.778
Torsion angles, period  3. refined              268    13.369    15.000
Torsion angles, period  4. refined                9    12.307    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   291     0.249     0.200
VDW repulsions.others                          1353     0.194     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             767     0.084     0.200
HBOND: refined_atoms                            218     0.198     0.200
HBOND.others                                      1     0.009     0.200
VDW repulsions: symmetry: refined_atoms           8     0.214     0.200
VDW repulsions: symmetry: others                 22     0.186     0.200
HBOND: symmetry: refined_atoms                   22     0.180     0.200
M. chain bond B values: refined atoms           746     1.675     1.363
M. chain bond B values: others                  746     1.672     1.363
M. chain angle B values: refined atoms          929     2.635     2.032
M. chain angle B values: others                 930     2.633     2.032
S. chain bond B values: refined atoms           811     2.989     1.758
S. chain bond B values: others                  810     2.982     1.757
S. chain angle B values: refined atoms         1177     4.615     2.470
S. chain angle B values: others                1178     4.613     2.470
Long range B values: refined atoms             1837     7.107    18.916
Long range B values: others                    1747     6.798    17.520
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0422, B  =   -0.0422
Partial structure    1: scale =     0.3854, B  =   43.5397
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.47 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.042    2898 100.00   461.4   469.8  0.16  0.17     130   455.1   466.2  0.20  0.21
 0.126    4865 100.00   309.7   296.1  0.17  0.15     277   312.9   292.1  0.22  0.20
 0.209    6167  99.97   209.6   194.9  0.16  0.14     336   217.2   203.4  0.20  0.17
 0.292    7250 100.00   117.4   127.4  0.23  0.17     396   116.5   126.5  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0423   2066   0.929    832   0.836   2898   0.902  0.954  0.9669  0.9739  0.9098  0.9413
  0.1257   4028   0.871    837   0.763   4865   0.853  0.995  0.9457  0.9586  0.8929  0.9410
  0.2090   5327   0.890    840   0.783   6167   0.876  1.038  0.9562  0.9636  0.9096  0.9422
  0.2924   6416   0.827    843   0.751   7259   0.818  0.862  0.9317  0.9422  0.8711  0.9143
 $$
Resolution limits                    =     41.964     1.730
Number of used reflections           =      21189
Percentage observed                  =    99.9866
Percentage of free reflections       =     5.1012
Overall R factor                     =     0.1740
Free R factor                        =     0.2204
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9464
Overall weighted R factor            =     0.1567
Free weighted R factor               =     0.1965
Overall weighted R2 factor           =     0.1885
Free weighted R2 factor              =     0.2314
Average correlation coefficient      =     0.9322
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9306
Cruickshanks DPI for coordinate error=     0.1116
DPI based on free R factor           =     0.1142
Overall figure of merit              =     0.8543
ML based su of positional parameters =     0.0697
ML based su of thermal parameters    =     2.1511
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.10
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1742   0.2202   0.838      110934.    6131.6   0.0127  0.946   1.813  1.053   0.089
       1   0.1743   0.2200   0.854      110409.    6122.0   0.0121  0.900   1.775  1.030   0.087
       2   0.1739   0.2200   0.855      110339.    6120.8   0.0127  0.947   1.803  1.046   0.089
       3   0.1739   0.2201   0.855      110328.    6120.9   0.0128  0.952   1.812  1.051   0.089
       4   0.1740   0.2202   0.855      110333.    6121.4   0.0128  0.953   1.815  1.053   0.089
       5   0.1740   0.2203   0.855      110330.    6121.5   0.0128  0.953   1.816  1.053   0.089
       6   0.1740   0.2204   0.854      110337.    6122.1   0.0128  0.954   1.817  1.054   0.089
       7   0.1740   0.2204   0.854      110338.    6122.2   0.0128  0.954   1.817  1.054   0.089
       8   0.1740   0.2205   0.854      110338.    6122.3   0.0128  0.953   1.817  1.054   0.089
       9   0.1740   0.2205   0.854      110339.    6122.3   0.0128  0.953   1.817  1.054   0.089
      10   0.1740   0.2204   0.854      110343.    6122.4   0.0128  0.953   1.817  1.054   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1742   0.1740
             R free    0.2202   0.2204
     Rms BondLength    0.0127   0.0128
      Rms BondAngle    1.8132   1.8170
     Rms ChirVolume    0.0890   0.0890
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.2s System:    0.2s Elapsed:     0:54