###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:59:46 


 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 1.50     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 3
  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_R03_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R03_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R03_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     3
  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  1.5000

  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_R03_1-60A.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=   2.037 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=   2.198 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=   1.816 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.218 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.387 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=   2.387 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=   2.095 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  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                            3
Number of "free" reflections       1642
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 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.= 0.881 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.29458296    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                40.5
Norm of Geom. positional gradient                80.5
Norm of X_ray B-factor gradient                  112.
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.468
Product of X_ray and Geom B-fact gradients     -0.332E+08
 Cosine of angle between them                      -0.889


Residuals: XRAY=     0.9779E+06 GEOM=     0.1304E+05 TOTAL=     0.9910E+06
 function value    990964.31    

-------------------------------------------------------------------------------
             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     1.778     1.644
Bond angles  : others                          3238     2.350     1.580
Torsion angles, period  1. refined              185     6.846     5.000
Torsion angles, period  2. refined               90    36.236    22.778
Torsion angles, period  3. refined              268    13.727    15.000
Torsion angles, period  4. refined                9    12.097    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   298     0.244     0.200
VDW repulsions.others                          1332     0.223     0.200
VDW; torsion: refined_atoms                     730     0.172     0.200
VDW; torsion.others                             701     0.082     0.200
HBOND: refined_atoms                            214     0.198     0.200
HBOND.others                                      2     0.043     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 24     0.175     0.200
HBOND: symmetry: refined_atoms                   18     0.202     0.200
HBOND: symmetry: others                           1     0.037     0.200
M. chain bond B values: refined atoms           746     1.689     1.511
M. chain bond B values: others                  746     1.686     1.511
M. chain angle B values: refined atoms          929     2.651     2.256
M. chain angle B values: others                 930     2.650     2.256
S. chain bond B values: refined atoms           811     3.111     1.916
S. chain bond B values: others                  810     3.104     1.916
S. chain angle B values: refined atoms         1177     4.804     2.705
S. chain angle B values: others                1178     4.802     2.704
Long range B values: refined atoms             1842     7.300    20.979
Long range B values: others                    1749     7.004    19.497
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    1.1809
Partial structure    1: scale =     0.3914, B  =   39.7281
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4336 100.00   404.2   414.8  0.17  0.18     211   424.0   424.1  0.19  0.20
 0.167    7421  99.97   227.6   208.0  0.18  0.16     377   227.5   209.1  0.20  0.18
 0.278    9443 100.00   123.3   113.5  0.21  0.19     467   130.7   119.5  0.24  0.22
 0.389   11054 100.00    50.0    62.3  0.41  0.37     587    51.0    63.4  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3227   0.913   1109   0.796   4336   0.883  0.946  0.9646  0.9696  0.8993  0.9367
  0.1670   6303   0.885   1118   0.787   7421   0.870  1.064  0.9515  0.9617  0.9055  0.9371
  0.2780   8309   0.828   1134   0.746   9443   0.818  1.016  0.9354  0.9410  0.8954  0.9265
  0.3890   9933   0.567   1133   0.496  11066   0.560  0.567  0.7754  0.7701  0.7644  0.7652
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32266
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8425
Overall R factor                     =     0.2073
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.8910
AverageFree Fourier shell correlation=     0.8856
Overall weighted R factor            =     0.1753
Free weighted R factor               =     0.1995
Overall weighted R2 factor           =     0.2051
Free weighted R2 factor              =     0.2348
Average correlation coefficient      =     0.8750
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9438
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0846
Overall figure of merit              =     0.7502
ML based su of positional parameters =     0.0706
ML based su of thermal parameters    =     2.0879
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156476.73       13036.521       990964.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35494933    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979149.00    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0733
Partial structure    1: scale =     0.3909, B  =   39.7302
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2329
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8988
Average correlation coefficient      =     0.8764
Overall figure of merit              =     0.7767
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155368.22       8149.0845       979149.00       990964.31    


     CGMAT cycle number =      3

 Weight matrix   0.36645007    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977915.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0323
Partial structure    1: scale =     0.3909, B  =   39.6212
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2061
Free R factor                        =     0.2319
Average Fourier shell correlation    =     0.9078
AverageFree Fourier shell correlation=     0.9024
Average correlation coefficient      =     0.8781
Overall figure of merit              =     0.7838
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155087.94       8667.2441       977915.56       979149.00    


     CGMAT cycle number =      4

 Weight matrix   0.36889079    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977624.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0261
Partial structure    1: scale =     0.3900, B  =   39.6731
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2059
Free R factor                        =     0.2316
Average Fourier shell correlation    =     0.9087
AverageFree Fourier shell correlation=     0.9031
Average correlation coefficient      =     0.8790
Overall figure of merit              =     0.7855
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155015.22       8830.6045       977624.44       977915.56    


     CGMAT cycle number =      5

 Weight matrix   0.33554137    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    889522.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0147
Partial structure    1: scale =     0.3901, B  =   39.7281
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2059
Free R factor                        =     0.2316
Average Fourier shell correlation    =     0.9088
AverageFree Fourier shell correlation=     0.9031
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7855
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154997.42       8901.7383       889522.25       977624.44    


     CGMAT cycle number =      6

 Weight matrix   0.30422151    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809499.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0178
Partial structure    1: scale =     0.3901, B  =   39.6768
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2062
Free R factor                        =     0.2318
Average Fourier shell correlation    =     0.9087
AverageFree Fourier shell correlation=     0.9030
Average correlation coefficient      =     0.8792
Overall figure of merit              =     0.7853
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155054.67       8639.4463       809499.19       889522.25    


     CGMAT cycle number =      7

 Weight matrix   0.30299997    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809576.19    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0174
Partial structure    1: scale =     0.3901, B  =   39.6323
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2321
Average Fourier shell correlation    =     0.9084
AverageFree Fourier shell correlation=     0.9027
Average correlation coefficient      =     0.8788
Overall figure of merit              =     0.7850
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    155136.64       8307.4082       809664.75       809499.19    

 fvalues    155136.64       8307.4082       809619.56       809590.56    
 fvalues    155136.64       8307.4082       809619.56       809590.56    


     CGMAT cycle number =      8

 Weight matrix   0.30291092    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809591.94    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0190
Partial structure    1: scale =     0.3902, B  =   39.6060
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2322
Average Fourier shell correlation    =     0.9084
AverageFree Fourier shell correlation=     0.9027
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7850
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155141.58       8282.4580       809608.88       809590.56    

 fvalues    155141.58       8282.4580       809613.38       809591.06    
 fvalues    155141.58       8282.4580       809613.38       809591.06    


     CGMAT cycle number =      9

 Weight matrix   0.30271953    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809610.50    

-------------------------------------------------------------------------------
             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
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0172
Partial structure    1: scale =     0.3902, B  =   39.5952
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2321
Average Fourier shell correlation    =     0.9084
AverageFree Fourier shell correlation=     0.9026
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7849
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155147.44       8275.4082       809634.69       809591.06    

 fvalues    155147.44       8275.4082       809626.44       809614.31    
 fvalues    155147.44       8275.4082       809626.44       809614.31    


     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.= 0.898 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.30274990    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                37.8
Norm of Geom. positional gradient                38.1
Norm of X_ray B-factor gradient                  95.9
Norm of Geom. B-factor gradient                  99.0
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.306E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8013E+06 GEOM=      8273.     TOTAL=     0.8096E+06
 function value    809609.13    

-------------------------------------------------------------------------------
             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     1.762     1.644
Bond angles  : others                          3238     1.483     1.580
Torsion angles, period  1. refined              185     6.855     5.000
Torsion angles, period  2. refined               90    36.110    22.778
Torsion angles, period  3. refined              268    13.296    15.000
Torsion angles, period  4. refined                9    12.048    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.242     0.200
VDW repulsions.others                          1347     0.196     0.200
VDW; torsion: refined_atoms                     726     0.171     0.200
VDW; torsion.others                             764     0.084     0.200
HBOND: refined_atoms                            218     0.193     0.200
HBOND.others                                      1     0.064     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 25     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.186     0.200
HBOND: symmetry: others                           1     0.033     0.200
M. chain bond B values: refined atoms           746     1.737     1.625
M. chain bond B values: others                  746     1.734     1.625
M. chain angle B values: refined atoms          929     2.708     2.429
M. chain angle B values: others                 930     2.707     2.429
S. chain bond B values: refined atoms           811     3.178     2.041
S. chain bond B values: others                  810     3.172     2.041
S. chain angle B values: refined atoms         1177     4.908     2.890
S. chain angle B values: others                1178     4.906     2.889
Long range B values: refined atoms             1843     7.258    22.354
Long range B values: others                    1749     6.973    20.801
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0180
Partial structure    1: scale =     0.3902, B  =   39.5833
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4336 100.00   404.7   415.4  0.17  0.18     211   424.6   425.6  0.19  0.20
 0.167    7421  99.97   228.0   208.2  0.18  0.16     377   227.8   209.4  0.20  0.18
 0.278    9443 100.00   123.5   113.9  0.21  0.19     467   130.8   119.8  0.24  0.22
 0.389   11054 100.00    50.1    62.3  0.41  0.36     587    51.0    63.3  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3227   0.930   1109   0.826   4336   0.903  0.949  0.9687  0.9737  0.8991  0.9370
  0.1670   6303   0.895   1118   0.799   7421   0.880  1.065  0.9536  0.9638  0.9058  0.9369
  0.2780   8309   0.849   1134   0.768   9443   0.839  1.019  0.9432  0.9498  0.8955  0.9283
  0.3890   9933   0.636   1133   0.563  11066   0.629  0.602  0.8139  0.8102  0.7653  0.7745
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32266
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8425
Overall R factor                     =     0.2067
Free R factor                        =     0.2321
Average Fourier shell correlation    =     0.9084
AverageFree Fourier shell correlation=     0.9026
Overall weighted R factor            =     0.1750
Free weighted R factor               =     0.2004
Overall weighted R2 factor           =     0.2043
Free weighted R2 factor              =     0.2378
Average correlation coefficient      =     0.8787
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9438
Cruickshanks DPI for coordinate error=     0.0855
DPI based on free R factor           =     0.0845
Overall figure of merit              =     0.7849
ML based su of positional parameters =     0.0632
ML based su of thermal parameters    =     1.8519
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    155146.98       8272.5840       809609.13       809614.31    

    ****                              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.= 0.898 id.= 3.000 dev= -2.10 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_R03_1-50A.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     1.761     1.644
Bond angles  : others                          3238     1.483     1.580
Torsion angles, period  1. refined              185     6.855     5.000
Torsion angles, period  2. refined               90    36.108    22.778
Torsion angles, period  3. refined              268    13.292    15.000
Torsion angles, period  4. refined                9    12.047    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.242     0.200
VDW repulsions.others                          1347     0.196     0.200
VDW; torsion: refined_atoms                     726     0.171     0.200
VDW; torsion.others                             762     0.084     0.200
HBOND: refined_atoms                            218     0.193     0.200
HBOND.others                                      1     0.064     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 25     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.187     0.200
HBOND: symmetry: others                           1     0.033     0.200
M. chain bond B values: refined atoms           746     1.736     1.625
M. chain bond B values: others                  746     1.733     1.625
M. chain angle B values: refined atoms          929     2.707     2.429
M. chain angle B values: others                 930     2.706     2.429
S. chain bond B values: refined atoms           811     3.177     2.041
S. chain bond B values: others                  810     3.170     2.040
S. chain angle B values: refined atoms         1177     4.906     2.889
S. chain angle B values: others                1178     4.904     2.889
Long range B values: refined atoms             1843     7.258    22.354
Long range B values: others                    1749     6.972    20.800
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0184
Partial structure    1: scale =     0.3902, B  =   39.5902
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4336 100.00   404.7   415.4  0.17  0.18     211   424.6   425.5  0.19  0.20
 0.167    7421  99.97   228.0   208.2  0.18  0.16     377   227.8   209.4  0.20  0.18
 0.278    9443 100.00   123.5   113.9  0.21  0.19     467   130.8   119.8  0.24  0.22
 0.389   11054 100.00    50.1    62.3  0.41  0.36     587    51.0    63.3  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3227   0.930   1109   0.826   4336   0.903  0.949  0.9687  0.9737  0.8992  0.9369
  0.1670   6303   0.895   1118   0.799   7421   0.880  1.065  0.9535  0.9638  0.9058  0.9369
  0.2780   8309   0.849   1134   0.768   9443   0.839  1.019  0.9432  0.9498  0.8955  0.9283
  0.3890   9933   0.636   1133   0.563  11066   0.629  0.602  0.8139  0.8102  0.7652  0.7746
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32266
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8425
Overall R factor                     =     0.2067
Free R factor                        =     0.2322
Average Fourier shell correlation    =     0.9084
AverageFree Fourier shell correlation=     0.9026
Overall weighted R factor            =     0.1750
Free weighted R factor               =     0.2004
Overall weighted R2 factor           =     0.2044
Free weighted R2 factor              =     0.2377
Average correlation coefficient      =     0.8787
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9438
Cruickshanks DPI for coordinate error=     0.0856
DPI based on free R factor           =     0.0845
Overall figure of merit              =     0.7849
ML based su of positional parameters =     0.0632
ML based su of thermal parameters    =     1.8519
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.93
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2073   0.2325   0.750      156477.    8094.3   0.0124  0.928   1.778  1.037   0.087
       1   0.2070   0.2329   0.777      155368.    8065.8   0.0124  0.928   1.755  1.024   0.088
       2   0.2061   0.2319   0.784      155088.    8057.2   0.0133  0.993   1.800  1.049   0.090
       3   0.2059   0.2316   0.785      155015.    8054.9   0.0134  1.002   1.818  1.060   0.091
       4   0.2059   0.2316   0.786      154997.    8054.6   0.0134  1.006   1.828  1.065   0.091
       5   0.2062   0.2318   0.785      155055.    8056.1   0.0128  0.962   1.802  1.049   0.089
       6   0.2066   0.2321   0.785      155134.    8058.4   0.0122  0.916   1.766  1.028   0.087
       7   0.2066   0.2322   0.785      155142.    8058.8   0.0122  0.914   1.763  1.026   0.087
       8   0.2067   0.2321   0.785      155147.    8059.0   0.0122  0.914   1.762  1.026   0.087
       9   0.2067   0.2321   0.785      155147.    8059.0   0.0122  0.914   1.762  1.026   0.087
      10   0.2067   0.2322   0.785      155147.    8059.0   0.0122  0.914   1.761  1.025   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2073   0.2067
             R free    0.2325   0.2322
     Rms BondLength    0.0124   0.0122
      Rms BondAngle    1.7776   1.7613
     Rms ChirVolume    0.0871   0.0866
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.9s System:    0.2s Elapsed:     1:01