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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: 15:25:07 


 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 1.80     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_1-81A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-80A.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_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  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  1.8000

  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_1-81A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.055 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.224 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=   1.861 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=   2.200 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=   2.416 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=   2.407 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=   2.147 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       1001
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 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.= 0.921 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.25519633    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                33.5
Norm of Geom. positional gradient                79.0
Norm of X_ray B-factor gradient                  112.
Norm of Geom. B-factor gradient                  114.
Product of X_ray and Geom posit. gradients     -0.107E+08
 Cosine of angle between them                      -0.416
Product of X_ray and Geom B-fact gradients     -0.388E+08
 Cosine of angle between them                      -0.937


Residuals: XRAY=     0.7055E+06 GEOM=     0.1308E+05 TOTAL=     0.7186E+06
 function value    718577.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.782     1.644
Bond angles  : others                          3238     2.355     1.580
Torsion angles, period  1. refined              185     6.976     5.000
Torsion angles, period  2. refined               90    35.921    22.778
Torsion angles, period  3. refined              268    13.432    15.000
Torsion angles, period  4. refined                9    11.522    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   297     0.244     0.200
VDW repulsions.others                          1320     0.220     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             722     0.080     0.200
HBOND: refined_atoms                            221     0.205     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms           9     0.209     0.200
VDW repulsions: symmetry: others                 22     0.207     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.613     1.284
M. chain bond B values: others                  746     1.611     1.284
M. chain angle B values: refined atoms          929     2.539     1.911
M. chain angle B values: others                 930     2.538     1.911
S. chain bond B values: refined atoms           811     2.732     1.644
S. chain bond B values: others                  810     2.729     1.644
S. chain angle B values: refined atoms         1177     4.260     2.312
S. chain angle B values: others                1178     4.258     2.312
Long range B values: refined atoms             1847     6.743    17.726
Long range B values: others                    1754     6.460    16.338
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0427
Partial structure    1: scale =     0.3780, B  =   46.7155
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.0   480.9  0.16  0.17     118   466.5   477.3  0.20  0.22
 0.116    4340 100.00   341.6   327.2  0.16  0.15     239   338.8   312.3  0.22  0.20
 0.193    5512  99.97   225.5   214.6  0.16  0.14     296   236.5   226.0  0.21  0.17
 0.270    6440 100.00   147.6   153.6  0.20  0.15     347   153.1   159.3  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.915    767   0.811   2575   0.884  0.954  0.9616  0.9696  0.9071  0.9403
  0.1161   3566   0.877    774   0.778   4340   0.859  0.995  0.9459  0.9613  0.8898  0.9450
  0.1931   4740   0.875    772   0.761   5512   0.859  1.011  0.9505  0.9587  0.9018  0.9380
  0.2701   5670   0.820    777   0.736   6447   0.810  0.899  0.9345  0.9445  0.8727  0.9252
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1675
Free R factor                        =     0.2182
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9451
Overall weighted R factor            =     0.1535
Free weighted R factor               =     0.1989
Overall weighted R2 factor           =     0.1865
Free weighted R2 factor              =     0.2380
Average correlation coefficient      =     0.9355
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9219
Cruickshanks DPI for coordinate error=     0.1224
DPI based on free R factor           =     0.1246
Overall figure of merit              =     0.8456
ML based su of positional parameters =     0.0803
ML based su of thermal parameters    =     2.5770
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100791.41       13081.571       718577.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.28453615    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711097.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0566
Partial structure    1: scale =     0.3781, B  =   46.7405
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1674
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9589
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100384.44       8450.9473       711097.94       718577.19    


     CGMAT cycle number =      3

 Weight matrix   0.28557804    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710854.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0474
Partial structure    1: scale =     0.3784, B  =   46.6647
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1670
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100320.73       8653.8711       710854.94       711097.94    


     CGMAT cycle number =      4

 Weight matrix   0.28552899    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710825.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0378
Partial structure    1: scale =     0.3784, B  =   46.5259
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1669
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9364
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100309.82       8701.0928       710825.81       710854.94    


     CGMAT cycle number =      5

 Weight matrix   0.28557140    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710787.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0374
Partial structure    1: scale =     0.3784, B  =   46.3449
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1669
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100302.75       8712.3066       710787.56       710825.81    


     CGMAT cycle number =      6

 Weight matrix   0.28543496    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710777.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0355
Partial structure    1: scale =     0.3784, B  =   46.2785
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1669
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100301.22       8713.2148       710777.69       710787.56    


     CGMAT cycle number =      7

 Weight matrix   0.28559795    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710733.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0371
Partial structure    1: scale =     0.3787, B  =   46.1399
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1669
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100295.78       8706.9258       710733.44       710777.69    


     CGMAT cycle number =      8

 Weight matrix   0.28541785    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710747.13    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0395
Partial structure    1: scale =     0.3789, B  =   46.1590
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1669
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    100299.66       8704.7393       710734.00       710733.44    
 fvalues    100299.66       8704.7393       710734.00       710758.31    


     CGMAT cycle number =      9

 Weight matrix   0.28542429    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710746.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0414
Partial structure    1: scale =     0.3784, B  =   46.1251
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1669
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100299.31       8694.8428       710746.00       710758.31    


     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.= 0.942 id.= 3.000 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.28524908    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                36.2
Norm of X_ray B-factor gradient                  120.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.127E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.468E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7021E+06 GEOM=      8696.     TOTAL=     0.7108E+06
 function value    710759.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.800     1.644
Bond angles  : others                          3238     1.473     1.580
Torsion angles, period  1. refined              185     6.930     5.000
Torsion angles, period  2. refined               90    35.792    22.778
Torsion angles, period  3. refined              268    13.399    15.000
Torsion angles, period  4. refined                9    11.969    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1360     0.190     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             795     0.083     0.200
HBOND: refined_atoms                            222     0.200     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.618     1.293
M. chain bond B values: others                  746     1.616     1.293
M. chain angle B values: refined atoms          929     2.552     1.926
M. chain angle B values: others                 930     2.551     1.925
S. chain bond B values: refined atoms           811     2.779     1.660
S. chain bond B values: others                  810     2.775     1.659
S. chain angle B values: refined atoms         1177     4.331     2.333
S. chain angle B values: others                1178     4.329     2.333
Long range B values: refined atoms             1848     6.856    17.960
Long range B values: others                    1751     6.486    16.472
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0377
Partial structure    1: scale =     0.3784, B  =   46.0820
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.4   481.5  0.16  0.17     118   466.9   477.6  0.20  0.22
 0.116    4340 100.00   341.9   327.0  0.16  0.15     239   339.1   312.8  0.22  0.20
 0.193    5512  99.97   225.7   214.6  0.16  0.14     296   236.7   225.8  0.21  0.18
 0.270    6440 100.00   147.7   153.8  0.19  0.15     347   153.2   159.1  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.927    767   0.825   2575   0.897  0.954  0.9642  0.9720  0.9071  0.9410
  0.1161   3566   0.879    774   0.781   4340   0.862  0.995  0.9469  0.9619  0.8900  0.9441
  0.1931   4740   0.877    772   0.762   5512   0.861  1.011  0.9513  0.9596  0.9027  0.9390
  0.2701   5670   0.852    777   0.767   6447   0.842  0.908  0.9404  0.9516  0.8734  0.9274
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1669
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Overall weighted R factor            =     0.1531
Free weighted R factor               =     0.1989
Overall weighted R2 factor           =     0.1860
Free weighted R2 factor              =     0.2379
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9223
Cruickshanks DPI for coordinate error=     0.1220
DPI based on free R factor           =     0.1245
Overall figure of merit              =     0.8594
ML based su of positional parameters =     0.0758
ML based su of thermal parameters    =     2.4070
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    100301.40       8695.7734       710754.75       710746.00    
 fvalues    100301.40       8695.7734       710754.75       710761.56    

    ****                              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.= 0.942 id.= 3.000 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.801     1.644
Bond angles  : others                          3238     1.473     1.580
Torsion angles, period  1. refined              185     6.927     5.000
Torsion angles, period  2. refined               90    35.784    22.778
Torsion angles, period  3. refined              268    13.398    15.000
Torsion angles, period  4. refined                9    11.983    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1356     0.190     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             796     0.083     0.200
HBOND: refined_atoms                            222     0.200     0.200
HBOND.others                                      1     0.027     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.618     1.293
M. chain bond B values: others                  746     1.616     1.293
M. chain angle B values: refined atoms          929     2.552     1.925
M. chain angle B values: others                 930     2.550     1.925
S. chain bond B values: refined atoms           811     2.778     1.660
S. chain bond B values: others                  810     2.775     1.659
S. chain angle B values: refined atoms         1177     4.331     2.333
S. chain angle B values: others                1178     4.329     2.333
Long range B values: refined atoms             1848     6.858    17.959
Long range B values: others                    1751     6.487    16.471
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0403
Partial structure    1: scale =     0.3781, B  =   46.1439
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.4   481.6  0.16  0.17     118   466.9   477.6  0.20  0.22
 0.116    4340 100.00   341.9   327.1  0.16  0.15     239   339.1   312.9  0.22  0.20
 0.193    5512  99.97   225.7   214.6  0.16  0.14     296   236.7   225.8  0.21  0.18
 0.270    6440 100.00   147.7   153.8  0.19  0.15     347   153.2   159.2  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.927    767   0.825   2575   0.897  0.954  0.9642  0.9721  0.9070  0.9410
  0.1161   3566   0.879    774   0.781   4340   0.862  0.995  0.9469  0.9619  0.8899  0.9440
  0.1931   4740   0.877    772   0.762   5512   0.861  1.011  0.9513  0.9596  0.9027  0.9390
  0.2701   5670   0.852    777   0.767   6447   0.842  0.908  0.9405  0.9516  0.8734  0.9274
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1669
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9480
Overall weighted R factor            =     0.1531
Free weighted R factor               =     0.1989
Overall weighted R2 factor           =     0.1860
Free weighted R2 factor              =     0.2379
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9223
Cruickshanks DPI for coordinate error=     0.1220
DPI based on free R factor           =     0.1245
Overall figure of merit              =     0.8594
ML based su of positional parameters =     0.0758
ML based su of thermal parameters    =     2.4070
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.24
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1675   0.2182   0.846      100791.    5520.6   0.0120  0.892   1.782  1.029   0.086
       1   0.1674   0.2175   0.859      100384.    5513.9   0.0115  0.854   1.752  1.011   0.084
       2   0.1670   0.2176   0.859      100321.    5513.2   0.0120  0.896   1.782  1.028   0.086
       3   0.1669   0.2178   0.859      100310.    5513.1   0.0121  0.901   1.790  1.033   0.086
       4   0.1669   0.2178   0.859      100303.    5512.8   0.0121  0.902   1.794  1.035   0.085
       5   0.1669   0.2178   0.859      100301.    5512.9   0.0121  0.903   1.796  1.036   0.085
       6   0.1669   0.2178   0.859      100296.    5512.6   0.0121  0.903   1.798  1.037   0.085
       7   0.1669   0.2178   0.859      100298.    5512.7   0.0121  0.903   1.799  1.037   0.085
       8   0.1669   0.2180   0.859      100299.    5512.9   0.0121  0.903   1.799  1.038   0.085
       9   0.1669   0.2180   0.859      100301.    5512.8   0.0121  0.903   1.800  1.038   0.085
      10   0.1669   0.2180   0.859      100299.    5512.8   0.0121  0.903   1.801  1.038   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1675   0.1669
             R free    0.2182   0.2180
     Rms BondLength    0.0120   0.0121
      Rms BondAngle    1.7820   1.8006
     Rms ChirVolume    0.0860   0.0852
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.5s System:    0.1s Elapsed:     0:47