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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: 16:05:32 


 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 19
  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_complete_R19_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R19_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_complete_R19_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:    19
  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_complete_R19_1-90A.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=   2.021 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.202 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.866 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=   2.193 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=   2.384 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=   2.412 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=   2.089 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:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           19
Number of "free" reflections        988
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.= 0.929 id.= 3.000 dev= -2.07 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   0.26842335    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.4
Norm of Geom. positional gradient                79.0
Norm of X_ray B-factor gradient                  133.
Norm of Geom. B-factor gradient                 0.216E+05
Product of X_ray and Geom posit. gradients     -0.106E+08
 Cosine of angle between them                      -0.344
Product of X_ray and Geom B-fact gradients     -0.422E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7072E+06 GEOM=     0.2624E+05 TOTAL=     0.7334E+06
 function value    733399.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.786     1.644
Bond angles  : others                          3242     2.336     1.582
Torsion angles, period  1. refined              184     6.964     5.000
Torsion angles, period  2. refined               90    37.118    22.778
Torsion angles, period  3. refined              268    14.060    15.000
Torsion angles, period  4. refined                9    11.378    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   311     0.262     0.200
VDW repulsions.others                          1348     0.229     0.200
VDW; torsion: refined_atoms                     712     0.172     0.200
VDW; torsion.others                             716     0.080     0.200
HBOND: refined_atoms                            234     0.210     0.200
HBOND.others                                      2     0.008     0.200
VDW repulsions: symmetry: refined_atoms          10     0.244     0.200
VDW repulsions: symmetry: others                 27     0.180     0.200
HBOND: symmetry: refined_atoms                   18     0.257     0.200
HBOND: symmetry: others                           1     0.108     0.200
M. chain bond B values: refined atoms           745     1.603     1.201
M. chain bond B values: others                  745     1.602     1.201
M. chain angle B values: refined atoms          926     2.543     1.780
M. chain angle B values: others                 927     2.542     1.780
S. chain bond B values: refined atoms           811     2.627     1.554
S. chain bond B values: others                  810     2.623     1.554
S. chain angle B values: refined atoms         1177     4.118     2.180
S. chain angle B values: others                1178     4.116     2.180
Long range B values: refined atoms             1863     7.041    17.020
Long range B values: others                    1765     6.687    15.625
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =    0.8781
Partial structure    1: scale =     0.3799, B  =   50.0380
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2554 100.00   472.9   480.4  0.16  0.17     139   495.5   502.4  0.19  0.20
 0.116    4360 100.00   341.7   327.0  0.16  0.15     219   356.0   341.4  0.22  0.20
 0.193    5519  99.97   226.5   215.7  0.15  0.13     289   229.6   220.9  0.20  0.17
 0.270    6447 100.00   148.3   155.5  0.22  0.17     340   148.0   156.5  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1800   0.920    754   0.824   2554   0.892  0.953  0.9680  0.9710  0.9265  0.9401
  0.1161   3583   0.877    777   0.766   4360   0.857  0.993  0.9464  0.9592  0.8893  0.9427
  0.1931   4754   0.893    765   0.773   5519   0.876  1.015  0.9558  0.9659  0.9051  0.9480
  0.2701   5680   0.813    774   0.730   6454   0.803  0.889  0.9187  0.9352  0.8438  0.9027
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18887
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9711
Overall R factor                     =     0.1694
Free R factor                        =     0.2179
Average Fourier shell correlation    =     0.9545
AverageFree Fourier shell correlation=     0.9426
Overall weighted R factor            =     0.1531
Free weighted R factor               =     0.1943
Overall weighted R2 factor           =     0.1854
Free weighted R2 factor              =     0.2197
Average correlation coefficient      =     0.9303
Overall correlation coefficient      =     0.9554
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1237
DPI based on free R factor           =     0.1244
Overall figure of merit              =     0.8490
ML based su of positional parameters =     0.0783
ML based su of thermal parameters    =     2.5337
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    101029.26       26239.270       733399.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.29370514    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    714159.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0784
Partial structure    1: scale =     0.3791, B  =   49.5206
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                     =     0.1685
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9329
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100588.98       10081.069       714159.75       733399.75    


     CGMAT cycle number =      3

 Weight matrix   0.29906908    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711990.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0522
Partial structure    1: scale =     0.3789, B  =   47.0140
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                     =     0.1673
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9468
Average correlation coefficient      =     0.9348
Overall figure of merit              =     0.8611
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100390.74       9298.9189       711990.06       714159.75    


     CGMAT cycle number =      4

 Weight matrix   0.30081150    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711214.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0312
Partial structure    1: scale =     0.3794, B  =   46.9478
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                        =     0.2146
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8616
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100310.72       9083.1006       711214.13       711990.06    


     CGMAT cycle number =      5

 Weight matrix   0.30148727    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710938.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0273
Partial structure    1: scale =     0.3797, B  =   47.0699
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                        =     0.2144
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8618
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100272.27       9076.3516       710938.25       711214.13    


     CGMAT cycle number =      6

 Weight matrix   0.30278534    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710795.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0257
Partial structure    1: scale =     0.3799, B  =   47.1326
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                        =     0.2140
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8622
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100248.76       9097.9658       710795.25       710938.25    


     CGMAT cycle number =      7

 Weight matrix   0.30319053    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710707.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0502
Partial structure    1: scale =     0.3800, B  =   47.1111
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                        =     0.2139
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9361
Overall figure of merit              =     0.8624
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100236.30       9097.6035       710707.75       710795.25    


     CGMAT cycle number =      8

 Weight matrix   0.30289748    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710681.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0405
Partial structure    1: scale =     0.3804, B  =   47.1418
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                        =     0.2138
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8624
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100230.29       9113.6670       710681.75       710707.75    


     CGMAT cycle number =      9

 Weight matrix   0.30319935    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710589.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0284
Partial structure    1: scale =     0.3841, B  =   47.6334
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                        =     0.2138
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9361
Overall figure of merit              =     0.8624
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100218.03       9106.8779       710589.13       710681.75    


     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.= 0.939 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   0.30306932    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.0
Norm of Geom. positional gradient                38.0
Norm of X_ray B-factor gradient                  123.
Norm of Geom. B-factor gradient                  125.
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.496E+08
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.7015E+06 GEOM=      9093.     TOTAL=     0.7106E+06
 function value    710574.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.817     1.644
Bond angles  : others                          3242     1.479     1.582
Torsion angles, period  1. refined              184     6.983     5.000
Torsion angles, period  2. refined               90    36.782    22.778
Torsion angles, period  3. refined              268    13.935    15.000
Torsion angles, period  4. refined                9    11.552    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   312     0.262     0.200
VDW repulsions.others                          1383     0.202     0.200
VDW; torsion: refined_atoms                     712     0.173     0.200
VDW; torsion.others                             797     0.084     0.200
HBOND: refined_atoms                            226     0.196     0.200
HBOND.others                                      1     0.027     0.200
VDW repulsions: symmetry: refined_atoms           9     0.225     0.200
VDW repulsions: symmetry: others                 29     0.157     0.200
HBOND: symmetry: refined_atoms                   22     0.231     0.200
HBOND: symmetry: others                           1     0.049     0.200
M. chain bond B values: refined atoms           745     1.637     1.286
M. chain bond B values: others                  745     1.636     1.286
M. chain angle B values: refined atoms          926     2.548     1.910
M. chain angle B values: others                 927     2.546     1.909
S. chain bond B values: refined atoms           811     2.807     1.663
S. chain bond B values: others                  810     2.805     1.662
S. chain angle B values: refined atoms         1177     4.375     2.335
S. chain angle B values: others                1178     4.374     2.335
Long range B values: refined atoms             1855     7.065    18.145
Long range B values: others                    1765     6.790    16.763
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0604
Partial structure    1: scale =     0.3842, B  =   47.6074
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2554 100.00   472.3   479.8  0.16  0.17     139   494.9   500.9  0.19  0.20
 0.116    4360 100.00   341.3   325.9  0.16  0.15     219   355.6   340.9  0.22  0.19
 0.193    5519  99.97   226.2   215.1  0.15  0.13     289   229.3   220.3  0.20  0.17
 0.270    6447 100.00   148.1   154.6  0.20  0.15     340   147.8   156.7  0.26  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1800   0.931    754   0.837   2554   0.903  0.955  0.9703  0.9728  0.9271  0.9388
  0.1161   3583   0.880    777   0.770   4360   0.861  0.993  0.9485  0.9602  0.8925  0.9421
  0.1931   4754   0.895    765   0.776   5519   0.879  1.015  0.9564  0.9658  0.9055  0.9450
  0.2701   5680   0.844    774   0.759   6454   0.833  0.904  0.9295  0.9483  0.8554  0.9235
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18887
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9711
Overall R factor                     =     0.1668
Free R factor                        =     0.2140
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9473
Overall weighted R factor            =     0.1532
Free weighted R factor               =     0.1919
Overall weighted R2 factor           =     0.1862
Free weighted R2 factor              =     0.2178
Average correlation coefficient      =     0.9362
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9334
Cruickshanks DPI for coordinate error=     0.1218
DPI based on free R factor           =     0.1221
Overall figure of merit              =     0.8624
ML based su of positional parameters =     0.0736
ML based su of thermal parameters    =     2.3523
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    100218.02       9092.5742       710574.75       710589.13    

    ****                              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.= 0.940 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_complete_R19_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.818     1.644
Bond angles  : others                          3242     1.479     1.582
Torsion angles, period  1. refined              184     6.985     5.000
Torsion angles, period  2. refined               90    36.773    22.778
Torsion angles, period  3. refined              268    13.939    15.000
Torsion angles, period  4. refined                9    11.553    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   313     0.262     0.200
VDW repulsions.others                          1381     0.202     0.200
VDW; torsion: refined_atoms                     712     0.173     0.200
VDW; torsion.others                             802     0.084     0.200
HBOND: refined_atoms                            225     0.196     0.200
HBOND.others                                      1     0.027     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 29     0.157     0.200
HBOND: symmetry: refined_atoms                   22     0.231     0.200
HBOND: symmetry: others                           1     0.045     0.200
M. chain bond B values: refined atoms           745     1.637     1.286
M. chain bond B values: others                  745     1.636     1.286
M. chain angle B values: refined atoms          926     2.547     1.909
M. chain angle B values: others                 927     2.546     1.908
S. chain bond B values: refined atoms           811     2.811     1.662
S. chain bond B values: others                  810     2.809     1.662
S. chain angle B values: refined atoms         1177     4.381     2.335
S. chain angle B values: others                1178     4.379     2.334
Long range B values: refined atoms             1855     7.061    18.128
Long range B values: others                    1767     6.796    16.765
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0561
Partial structure    1: scale =     0.3842, B  =   47.5276
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2554 100.00   472.3   479.7  0.16  0.17     139   494.9   500.9  0.19  0.20
 0.116    4360 100.00   341.3   325.9  0.16  0.15     219   355.6   340.9  0.22  0.19
 0.193    5519  99.97   226.2   215.1  0.15  0.13     289   229.3   220.2  0.20  0.17
 0.270    6447 100.00   148.1   154.6  0.20  0.15     340   147.8   156.7  0.26  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1800   0.931    754   0.837   2554   0.903  0.955  0.9703  0.9729  0.9271  0.9388
  0.1161   3583   0.880    777   0.770   4360   0.861  0.993  0.9485  0.9603  0.8925  0.9421
  0.1931   4754   0.895    765   0.776   5519   0.879  1.015  0.9563  0.9657  0.9053  0.9450
  0.2701   5680   0.844    774   0.759   6454   0.833  0.904  0.9295  0.9484  0.8553  0.9237
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18887
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9711
Overall R factor                     =     0.1668
Free R factor                        =     0.2139
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9473
Overall weighted R factor            =     0.1532
Free weighted R factor               =     0.1918
Overall weighted R2 factor           =     0.1862
Free weighted R2 factor              =     0.2176
Average correlation coefficient      =     0.9362
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9334
Cruickshanks DPI for coordinate error=     0.1218
DPI based on free R factor           =     0.1221
Overall figure of merit              =     0.8624
ML based su of positional parameters =     0.0736
ML based su of thermal parameters    =     2.3523
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.69
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1694   0.2179   0.849      101029.    5472.5   0.0124  0.917   1.786  1.031   0.084
       1   0.1685   0.2164   0.859      100589.    5459.5   0.0121  0.894   1.764  1.017   0.086
       2   0.1673   0.2153   0.861      100391.    5452.9   0.0126  0.936   1.787  1.029   0.088
       3   0.1670   0.2146   0.862      100311.    5449.6   0.0127  0.943   1.799  1.035   0.088
       4   0.1669   0.2144   0.862      100272.    5448.3   0.0128  0.946   1.806  1.039   0.088
       5   0.1669   0.2140   0.862      100249.    5447.3   0.0128  0.947   1.810  1.040   0.088
       6   0.1669   0.2139   0.862      100236.    5447.3   0.0128  0.948   1.813  1.042   0.088
       7   0.1669   0.2138   0.862      100230.    5447.3   0.0128  0.948   1.815  1.043   0.088
       8   0.1669   0.2138   0.862      100218.    5447.0   0.0128  0.948   1.816  1.043   0.088
       9   0.1668   0.2140   0.862      100218.    5447.3   0.0128  0.948   1.817  1.043   0.088
      10   0.1668   0.2139   0.862      100216.    5447.3   0.0128  0.947   1.818  1.044   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1694   0.1668
             R free    0.2179   0.2139
     Rms BondLength    0.0124   0.0128
      Rms BondAngle    1.7859   1.8184
     Rms ChirVolume    0.0845   0.0880
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.8s System:    0.1s Elapsed:     0:46