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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: 13:06:51 


 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 1.97     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-01A_R00_1-98A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-97A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-97A.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       0.0644
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9700
  Estimated number of reflections :      19845
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.9700

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_step0-01A_R00_1-98A.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=   1.993 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=   2.205 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=   1.847 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=   2.222 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=   2.379 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=   2.451 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:22-OCT-19
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            0
Number of "free" reflections        772
Number of   all  reflections      15292
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          15292

   Current auto weighting coefficient =    7.4246039    

 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.= 0.915 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Weight matrix   0.18220341    
 Actual weight    7.4246039      is applied to the X-ray term
Norm of X_ray positional gradient                29.4
Norm of Geom. positional gradient                77.0
Norm of X_ray B-factor gradient                  98.6
Norm of Geom. B-factor gradient                  97.6
Product of X_ray and Geom posit. gradients     -0.773E+07
 Cosine of angle between them                      -0.352
Product of X_ray and Geom B-fact gradients     -0.288E+08
 Cosine of angle between them                      -0.926


Residuals: XRAY=     0.5958E+06 GEOM=     0.1230E+05 TOTAL=     0.6081E+06
 function value    608125.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.686     1.644
Bond angles  : others                          3238     2.337     1.580
Torsion angles, period  1. refined              185     7.159     5.000
Torsion angles, period  2. refined               90    36.172    22.778
Torsion angles, period  3. refined              268    14.587    15.000
Torsion angles, period  4. refined                9    11.774    15.000
Chiral centres: refined atoms                   196     0.081     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   304     0.243     0.200
VDW repulsions.others                          1344     0.219     0.200
VDW; torsion: refined_atoms                     712     0.169     0.200
VDW; torsion.others                             709     0.079     0.200
HBOND: refined_atoms                            229     0.210     0.200
HBOND.others                                      2     0.062     0.200
Metal-ion: refined_atoms                          1     0.007     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 24     0.191     0.200
HBOND: symmetry: refined_atoms                   16     0.222     0.200
M. chain bond B values: refined atoms           746     1.467     1.190
M. chain bond B values: others                  746     1.466     1.190
M. chain angle B values: refined atoms          929     2.402     1.771
M. chain angle B values: others                 930     2.401     1.771
S. chain bond B values: refined atoms           811     2.320     1.499
S. chain bond B values: others                  810     2.317     1.499
S. chain angle B values: refined atoms         1177     3.704     2.111
S. chain angle B values: others                1178     3.703     2.111
Long range B values: refined atoms             1858     6.685    16.561
Long range B values: others                    1760     6.315    15.159
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1712
Partial structure    1: scale =     0.3731, B  =   46.6956
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2002 100.00   484.6   486.9  0.16  0.17      91   475.4   486.6  0.20  0.22
 0.097    3359 100.00   413.7   395.4  0.16  0.15     169   411.7   380.7  0.23  0.21
 0.161    4202  99.96   259.0   257.1  0.16  0.14     249   274.9   267.8  0.23  0.19
 0.226    4950 100.00   212.1   209.9  0.16  0.13     263   216.0   218.9  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0327   1363   0.908    639   0.812   2002   0.877  0.964  0.9616  0.9689  0.9166  0.9426
  0.0970   2710   0.886    649   0.762   3359   0.862  0.999  0.9446  0.9618  0.8770  0.9433
  0.1613   3561   0.849    641   0.763   4202   0.836  0.964  0.9394  0.9535  0.8765  0.9400
  0.2255   4303   0.866    652   0.748   4955   0.851  0.965  0.9440  0.9573  0.8764  0.9407
 $$
Resolution limits                    =     41.964     1.970
Number of used reflections           =      14518
Percentage observed                  =    99.9804
Percentage of free reflections       =     5.0491
Overall R factor                     =     0.1586
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9447
Overall weighted R factor            =     0.1493
Free weighted R factor               =     0.2039
Overall weighted R2 factor           =     0.1816
Free weighted R2 factor              =     0.2435
Average correlation coefficient      =     0.9413
Overall correlation coefficient      =     0.9541
Free correlation coefficient         =     0.9066
Cruickshanks DPI for coordinate error=     0.1608
DPI based on free R factor           =     0.1567
Overall figure of merit              =     0.8527
ML based su of positional parameters =     0.0979
ML based su of thermal parameters    =     3.3609
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    80249.859       12302.355       608125.81      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.18993989    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602425.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1533
Partial structure    1: scale =     0.3725, B  =   46.5921
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9418
Overall figure of merit              =     0.8566
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    80083.438       7838.0781       602425.88       608125.81    


     CGMAT cycle number =      3

 Weight matrix   0.19032153    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602342.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1366
Partial structure    1: scale =     0.3728, B  =   46.6747
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.56 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2187
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9461
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8569
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    80066.586       7879.5205       602342.19       602425.88    


     CGMAT cycle number =      4

 Weight matrix   0.19038253    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602294.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1312
Partial structure    1: scale =     0.3729, B  =   46.5568
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9461
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8569
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    80060.188       7879.2461       602294.44       602342.19    


     CGMAT cycle number =      5

 Weight matrix   0.19038489    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602245.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1368
Partial structure    1: scale =     0.3728, B  =   46.5276
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8570
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    80055.344       7866.0225       602245.25       602294.44    


     CGMAT cycle number =      6

 Weight matrix   0.19021672    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602222.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1396
Partial structure    1: scale =     0.3730, B  =   46.3439
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2183
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9461
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8570
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    80053.828       7855.0000       602222.94       602245.25    


     CGMAT cycle number =      7

 Weight matrix   0.18993872    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602207.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1466
Partial structure    1: scale =     0.3732, B  =   46.3546
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9461
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8569
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    80053.945       7838.6895       602207.50       602222.94    


     CGMAT cycle number =      8

 Weight matrix   0.18953823    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602223.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1543
Partial structure    1: scale =     0.3733, B  =   46.3136
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8568
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    80057.305       7828.0264       602206.44       602207.50    
 fvalues    80057.305       7828.0264       602206.44       602221.75    


     CGMAT cycle number =      9

 Weight matrix   0.18932270    
 Actual weight    7.4246039      is applied to the X-ray term


 function value    602243.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1416
Partial structure    1: scale =     0.3733, B  =   46.3162
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9420
Overall figure of merit              =     0.8567
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    80060.922       7822.7803       602229.19       602221.75    
 fvalues    80060.922       7822.7803       602229.19       602243.38    


     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.= 0.930 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        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  150
 Weight matrix   0.18913916    
 Actual weight    7.4246039      is applied to the X-ray term
Norm of X_ray positional gradient                29.5
Norm of Geom. positional gradient                29.5
Norm of X_ray B-factor gradient                  97.8
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.842E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.320E+08
 Cosine of angle between them                      -0.983


Residuals: XRAY=     0.5945E+06 GEOM=      7815.     TOTAL=     0.6023E+06
 function value    602265.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.678     1.644
Bond angles  : others                          3238     1.401     1.580
Torsion angles, period  1. refined              185     7.088     5.000
Torsion angles, period  2. refined               90    36.479    22.778
Torsion angles, period  3. refined              268    14.437    15.000
Torsion angles, period  4. refined                9    11.490    15.000
Chiral centres: refined atoms                   196     0.080     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.241     0.200
VDW repulsions.others                          1360     0.192     0.200
VDW; torsion: refined_atoms                     710     0.169     0.200
VDW; torsion.others                             786     0.082     0.200
HBOND: refined_atoms                            235     0.209     0.200
HBOND.others                                      1     0.079     0.200
Metal-ion: refined_atoms                          1     0.018     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 24     0.175     0.200
HBOND: symmetry: refined_atoms                   18     0.226     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           746     1.480     1.189
M. chain bond B values: others                  746     1.479     1.189
M. chain angle B values: refined atoms          929     2.418     1.770
M. chain angle B values: others                 930     2.416     1.769
S. chain bond B values: refined atoms           811     2.312     1.498
S. chain bond B values: others                  810     2.309     1.498
S. chain angle B values: refined atoms         1177     3.696     2.110
S. chain angle B values: others                1178     3.695     2.109
Long range B values: refined atoms             1863     6.722    16.655
Long range B values: others                    1760     6.325    15.188
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1445
Partial structure    1: scale =     0.3733, B  =   46.3094
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2002 100.00   485.3   487.6  0.16  0.17      91   476.1   487.9  0.20  0.22
 0.097    3359 100.00   414.3   395.5  0.16  0.15     169   412.3   381.1  0.22  0.21
 0.161    4202  99.96   259.4   257.5  0.16  0.14     249   275.3   267.2  0.22  0.19
 0.226    4950 100.00   212.4   210.3  0.15  0.12     263   216.3   219.5  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0327   1363   0.918    639   0.825   2002   0.889  0.964  0.9639  0.9712  0.9159  0.9434
  0.0970   2710   0.890    649   0.769   3359   0.867  0.999  0.9462  0.9629  0.8784  0.9430
  0.1613   3561   0.850    641   0.764   4202   0.837  0.964  0.9396  0.9537  0.8771  0.9391
  0.2255   4303   0.869    652   0.750   4955   0.854  0.965  0.9455  0.9590  0.8780  0.9431
 $$
Resolution limits                    =     41.964     1.970
Number of used reflections           =      14518
Percentage observed                  =    99.9804
Percentage of free reflections       =     5.0491
Overall R factor                     =     0.1580
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9459
Overall weighted R factor            =     0.1489
Free weighted R factor               =     0.2027
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2436
Average correlation coefficient      =     0.9420
Overall correlation coefficient      =     0.9543
Free correlation coefficient         =     0.9073
Cruickshanks DPI for coordinate error=     0.1602
DPI based on free R factor           =     0.1557
Overall figure of merit              =     0.8566
ML based su of positional parameters =     0.0959
ML based su of thermal parameters    =     3.3049
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    80065.203       7814.6177       602253.69       602243.38    
 fvalues    80065.203       7814.6177       602253.69       602267.06    

    ****                              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.= 0.930 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-97A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.678     1.644
Bond angles  : others                          3238     1.401     1.580
Torsion angles, period  1. refined              185     7.086     5.000
Torsion angles, period  2. refined               90    36.501    22.778
Torsion angles, period  3. refined              268    14.437    15.000
Torsion angles, period  4. refined                9    11.462    15.000
Chiral centres: refined atoms                   196     0.080     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.241     0.200
VDW repulsions.others                          1356     0.192     0.200
VDW; torsion: refined_atoms                     710     0.169     0.200
VDW; torsion.others                             787     0.082     0.200
HBOND: refined_atoms                            234     0.209     0.200
HBOND.others                                      1     0.078     0.200
Metal-ion: refined_atoms                          1     0.018     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 24     0.175     0.200
HBOND: symmetry: refined_atoms                   18     0.227     0.200
HBOND: symmetry: others                           1     0.009     0.200
M. chain bond B values: refined atoms           746     1.480     1.189
M. chain bond B values: others                  746     1.480     1.190
M. chain angle B values: refined atoms          929     2.418     1.770
M. chain angle B values: others                 930     2.417     1.770
S. chain bond B values: refined atoms           811     2.310     1.498
S. chain bond B values: others                  810     2.307     1.498
S. chain angle B values: refined atoms         1177     3.694     2.110
S. chain angle B values: others                1178     3.692     2.109
Long range B values: refined atoms             1861     6.707    16.639
Long range B values: others                    1759     6.314    15.185
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0397, B  =   -0.1412
Partial structure    1: scale =     0.3732, B  =   46.1545
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2002 100.00   485.2   487.6  0.16  0.17      91   476.0   487.9  0.20  0.22
 0.097    3359 100.00   414.2   395.4  0.16  0.15     169   412.2   381.1  0.22  0.21
 0.161    4202  99.96   259.3   257.5  0.16  0.14     249   275.3   267.1  0.22  0.19
 0.226    4950 100.00   212.4   210.2  0.15  0.12     263   216.3   219.5  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0327   1363   0.918    639   0.825   2002   0.889  0.964  0.9639  0.9712  0.9159  0.9435
  0.0970   2710   0.890    649   0.769   3359   0.867  0.999  0.9463  0.9630  0.8786  0.9431
  0.1613   3561   0.850    641   0.764   4202   0.837  0.964  0.9395  0.9536  0.8771  0.9390
  0.2255   4303   0.869    652   0.750   4955   0.854  0.965  0.9455  0.9589  0.8780  0.9431
 $$
Resolution limits                    =     41.964     1.970
Number of used reflections           =      14518
Percentage observed                  =    99.9804
Percentage of free reflections       =     5.0491
Overall R factor                     =     0.1579
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9459
Overall weighted R factor            =     0.1489
Free weighted R factor               =     0.2026
Overall weighted R2 factor           =     0.1810
Free weighted R2 factor              =     0.2436
Average correlation coefficient      =     0.9420
Overall correlation coefficient      =     0.9543
Free correlation coefficient         =     0.9074
Cruickshanks DPI for coordinate error=     0.1602
DPI based on free R factor           =     0.1557
Overall figure of merit              =     0.8566
ML based su of positional parameters =     0.0959
ML based su of thermal parameters    =     3.3049
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.13
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1586   0.2198   0.853       80250.    4428.2   0.0110  0.803   1.686  0.976   0.081
       1   0.1585   0.2192   0.857       80083.    4426.3   0.0107  0.782   1.665  0.964   0.080
       2   0.1582   0.2187   0.857       80067.    4425.7   0.0109  0.803   1.678  0.972   0.081
       3   0.1580   0.2186   0.857       80060.    4425.5   0.0110  0.805   1.681  0.974   0.081
       4   0.1580   0.2184   0.857       80055.    4425.0   0.0110  0.805   1.681  0.974   0.080
       5   0.1580   0.2183   0.857       80054.    4424.7   0.0110  0.806   1.681  0.975   0.080
       6   0.1580   0.2184   0.857       80054.    4424.9   0.0110  0.805   1.680  0.974   0.080
       7   0.1580   0.2184   0.857       80057.    4425.3   0.0110  0.805   1.679  0.974   0.080
       8   0.1580   0.2184   0.857       80061.    4425.7   0.0110  0.805   1.679  0.974   0.080
       9   0.1580   0.2184   0.857       80065.    4425.9   0.0110  0.805   1.678  0.974   0.080
      10   0.1579   0.2184   0.857       80060.    4425.8   0.0110  0.804   1.678  0.974   0.080
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1586   0.1579
             R free    0.2198   0.2184
     Rms BondLength    0.0110   0.0110
      Rms BondAngle    1.6863   1.6780
     Rms ChirVolume    0.0808   0.0803
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.4s System:    0.1s Elapsed:     0:47