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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: malyma  Run date: 12/ 3/2021 Run time: 11:08:23 


 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.

<!--SUMMARY_END--></FONT></B>
 $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 47.32 1.90     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 5
  Data line--- ncyc 10
  Data line--- weight matrix 0.0600
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: poli67_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - poli_webinar_R00_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_webinar_R00_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli_webinar_R00_1-90A.mtz

Cell from mtz :    58.265    79.758    94.643    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21

  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:     5       0.0554
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  1.9000
  Estimated number of reflections :      45570
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.0600
  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:    47.3245  1.9000

  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 :poli_webinar_R00_2-00A.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    :    2286
  Number of residues :     307
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  BBB  is missing in the structure
  ATTENTION: atom:OXT  THR                70  BBB  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  BBB  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :    2331
  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   1.0317


 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:      4485         0      4485
               Angles:      8175         0      8175
              Chirals:       284         0       284
               Planes:       646         0       646
             Torsions:      2321         0      2321
            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       1724
Number of   all  reflections      35468
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          35468

   Current auto weighting coefficient =    7.2500257    

 mode : HKRF


######  TLS Group Definitions ######


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix   5.99999987E-02
 Actual weight    22.706661      is applied to the X-ray term
Norm of X_ray positional gradient                35.4
Norm of Geom. positional gradient                77.7
Norm of X_ray B-factor gradient                  36.4
Norm of Geom. B-factor gradient                  32.7
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.385
Product of X_ray and Geom B-fact gradients     -0.422E+07
 Cosine of angle between them                      -0.792


Residuals: XRAY=     0.2994E+07 GEOM=     0.1880E+05 TOTAL=     0.3013E+07
 function value    3012681.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.983     1.648
Bond angles  : others                          5121     2.287     1.582
Torsion angles, period  1. refined              265     7.661     5.000
Torsion angles, period  2. refined              135    32.865    22.370
Torsion angles, period  3. refined              475    20.687    15.000
Torsion angles, period  4. refined               19    20.959    15.000
Chiral centres: refined atoms                   284     0.087     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.015     0.020
VDW repulsions: refined_atoms                   544     0.234     0.200
VDW repulsions.others                          1987     0.227     0.200
VDW; torsion: refined_atoms                    1099     0.175     0.200
VDW; torsion.others                            1046     0.083     0.200
HBOND: refined_atoms                             59     0.193     0.200
HBOND.others                                      1     0.042     0.200
VDW repulsions: symmetry: refined_atoms          11     0.216     0.200
VDW repulsions: symmetry: others                 32     0.243     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     7.985     6.884
M. chain bond B values: others                 1074     7.967     6.875
M. chain angle B values: refined atoms         1335    10.170    10.268
M. chain angle B values: others                1336    10.169    10.277
S. chain bond B values: refined atoms          1209     9.347     7.714
S. chain bond B values: others                 1207     9.346     7.706
S. chain angle B values: refined atoms         1719    12.959    11.219
S. chain angle B values: others                1719    12.951    11.219
Long range B values: refined atoms             2626    14.895    78.964
Long range B values: others                    2625    14.911    78.988
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4878, B  =   -1.3483
Partial structure    1: scale =     0.3815, B  =   55.7701
Overall anisotropic scale factors
   B11 =   4.91 B22 =  -1.57 B33 =  -3.34 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   271.7   268.6  0.20  0.20     153   258.8   253.6  0.28  0.29
 0.083    5552  99.88   134.6   123.4  0.20  0.19     305   134.1   124.1  0.28  0.26
 0.139    7124  99.77    44.8    46.0  0.28  0.24     364    46.5    49.4  0.36  0.33
 0.194    8355  99.91    24.3    21.5  0.39  0.38     424    24.2    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.6  0.56  0.56     428    20.0    10.0  0.55  0.55
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.822    698   0.753   3240   0.807  0.935  0.9119  0.9445  0.8543  0.9275
  0.0834   4838   0.802    714   0.708   5552   0.790  0.995  0.9026  0.9276  0.8565  0.9344
  0.1387   6411   0.656    713   0.609   7124   0.651  0.791  0.8093  0.8338  0.7202  0.8715
  0.1940   7643   0.407    712   0.356   8355   0.402  0.550  0.5158  0.5113  0.7062  0.7076
  0.2493   7833   0.303    643   0.296   8476   0.302  0.684  0.3280  0.3073  0.4162  0.4685
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2548
Free R factor                        =     0.3266
Average Fourier shell correlation    =     0.6421
AverageFree Fourier shell correlation=     0.6383
Overall weighted R factor            =     0.2205
Free weighted R factor               =     0.2948
Overall weighted R2 factor           =     0.2280
Free weighted R2 factor              =     0.3120
Average correlation coefficient      =     0.7416
Overall correlation coefficient      =     0.9614
Free correlation coefficient         =     0.9221
Cruickshanks DPI for coordinate error=     0.1547
DPI based on free R factor           =     0.1684
Overall figure of merit              =     0.5362
ML based su of positional parameters =     0.2719
ML based su of thermal parameters    =    11.3720
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Not converging with gamma equal    0.0000000    
 Trying gamma equal   5.24999984E-02
 Gamma decreased to   4.19999994E-02
 fvalues    131850.25       18802.676       3012681.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   5.99999949E-02
 Actual weight    21.089006      is applied to the X-ray term


 function value    2787594.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4882, B  =   -0.2470
Partial structure    1: scale =     0.3853, B  =   55.6462
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.56 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2548
Free R factor                        =     0.3253
Average Fourier shell correlation    =     0.6427
AverageFree Fourier shell correlation=     0.6397
Average correlation coefficient      =     0.7424
Overall figure of merit              =     0.5373
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    131586.31       12570.283       2787594.8       3012681.8    


     CGMAT cycle number =      3

 Weight matrix   5.99999987E-02
 Actual weight    20.664665      is applied to the X-ray term


 function value    2731962.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4861, B  =   -0.1909
Partial structure    1: scale =     0.3852, B  =   54.9023
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.55 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2549
Free R factor                        =     0.3262
Average Fourier shell correlation    =     0.6469
AverageFree Fourier shell correlation=     0.6433
Average correlation coefficient      =     0.7421
Overall figure of merit              =     0.5447
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    131592.44       12648.723       2731962.5       2787594.8    


     CGMAT cycle number =      4

 Weight matrix   5.99999987E-02
 Actual weight    22.165258      is applied to the X-ray term


 function value    2930598.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4864, B  =   -0.1047
Partial structure    1: scale =     0.3854, B  =   54.6975
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.55 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2549
Free R factor                        =     0.3253
Average Fourier shell correlation    =     0.6345
AverageFree Fourier shell correlation=     0.6324
Average correlation coefficient      =     0.7426
Overall figure of merit              =     0.5202
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02


 fvalues    131639.45       12500.517       2930130.0       2731962.5    
 fvalues    131639.45       12500.517       2930130.0       2930323.0    


     CGMAT cycle number =      5

 Weight matrix   5.99999987E-02
 Actual weight    22.085890      is applied to the X-ray term


 function value    2920136.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4866, B  =   -0.0806
Partial structure    1: scale =     0.3854, B  =   54.5717
Overall anisotropic scale factors
   B11 =   4.85 B22 =  -1.54 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3263
Average Fourier shell correlation    =     0.6359
AverageFree Fourier shell correlation=     0.6334
Average correlation coefficient      =     0.7415
Overall figure of merit              =     0.5214
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03
 fvalues    131628.39       13005.667       2920136.0       2930323.0    


     CGMAT cycle number =      6

 Weight matrix   5.99999949E-02
 Actual weight    22.148434      is applied to the X-ray term


 function value    2927861.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4877, B  =   -0.1004
Partial structure    1: scale =     0.3855, B  =   54.6656
Overall anisotropic scale factors
   B11 =   4.84 B22 =  -1.55 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3262
Average Fourier shell correlation    =     0.6355
AverageFree Fourier shell correlation=     0.6330
Average correlation coefficient      =     0.7414
Overall figure of merit              =     0.5205
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Not converging with gamma equal   8.71641375E-03
 Trying gamma equal   4.29446921E-02
 Gamma decreased to   3.60990353E-02


 fvalues    131610.00       12940.002       2927724.0       2920136.0    
 fvalues    131610.00       12940.002       2927724.0       2927895.3    


     CGMAT cycle number =      7

 Weight matrix   5.99999987E-02
 Actual weight    22.403631      is applied to the X-ray term


 function value    2961610.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4879, B  =   -0.0492
Partial structure    1: scale =     0.3857, B  =   54.7303
Overall anisotropic scale factors
   B11 =   4.84 B22 =  -1.54 B33 =  -3.29 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2542
Free R factor                        =     0.3265
Average Fourier shell correlation    =     0.6342
AverageFree Fourier shell correlation=     0.6316
Average correlation coefficient      =     0.7412
Overall figure of merit              =     0.5187
-----------------------------------------------------------------------------
 Trying gamma equal   3.60990353E-02
 Gamma decreased to   2.98757106E-02


 fvalues    131597.09       13057.291       2960888.8       2927895.3    
 fvalues    131597.09       13057.291       2960888.8       2961310.0    


     CGMAT cycle number =      8

 Weight matrix   5.99999949E-02
 Actual weight    22.206728      is applied to the X-ray term


 function value    2935128.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4889, B  =   -0.0512
Partial structure    1: scale =     0.3859, B  =   54.8689
Overall anisotropic scale factors
   B11 =   4.83 B22 =  -1.54 B33 =  -3.28 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2541
Free R factor                        =     0.3269
Average Fourier shell correlation    =     0.6359
AverageFree Fourier shell correlation=     0.6330
Average correlation coefficient      =     0.7409
Overall figure of merit              =     0.5206
-----------------------------------------------------------------------------
 Trying gamma equal   2.98757106E-02
 Gamma decreased to   2.42181439E-02
 fvalues    131583.56       13087.963       2935128.5       2961310.0    


     CGMAT cycle number =      9

 Weight matrix   5.99999987E-02
 Actual weight    22.259308      is applied to the X-ray term


 function value    2942334.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4887, B  =   -0.1225
Partial structure    1: scale =     0.3858, B  =   54.9714
Overall anisotropic scale factors
   B11 =   4.82 B22 =  -1.54 B33 =  -3.29 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2542
Free R factor                        =     0.3272
Average Fourier shell correlation    =     0.6357
AverageFree Fourier shell correlation=     0.6328
Average correlation coefficient      =     0.7410
Overall figure of merit              =     0.5202
-----------------------------------------------------------------------------
 Trying gamma equal   2.42181439E-02
 Gamma decreased to   1.90749019E-02


 fvalues    131601.84       13084.963       2942431.0       2935128.5    
 fvalues    131601.84       13084.963       2942431.0       2942451.0    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix   5.99999987E-02
 Actual weight    22.266470      is applied to the X-ray term
Norm of X_ray positional gradient                35.8
Norm of Geom. positional gradient                35.8
Norm of X_ray B-factor gradient                  36.2
Norm of Geom. B-factor gradient                  36.9
Product of X_ray and Geom posit. gradients     -0.172E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.597E+07
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.2930E+07 GEOM=     0.1312E+05 TOTAL=     0.2943E+07
 function value    2943005.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     2.065     1.648
Bond angles  : others                          5121     1.421     1.582
Torsion angles, period  1. refined              265     7.886     5.000
Torsion angles, period  2. refined              135    33.086    22.370
Torsion angles, period  3. refined              475    21.354    15.000
Torsion angles, period  4. refined               19    19.990    15.000
Chiral centres: refined atoms                   284     0.090     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   554     0.242     0.200
VDW repulsions.others                          2090     0.202     0.200
VDW; torsion: refined_atoms                    1105     0.176     0.200
VDW; torsion.others                            1134     0.093     0.200
HBOND: refined_atoms                             63     0.201     0.200
HBOND.others                                      1     0.299     0.200
VDW repulsions: symmetry: refined_atoms           9     0.236     0.200
VDW repulsions: symmetry: others                 38     0.215     0.200
HBOND: symmetry: refined_atoms                    2     0.132     0.200
M. chain bond B values: refined atoms          1075     8.174     6.761
M. chain bond B values: others                 1074     8.168     6.753
M. chain angle B values: refined atoms         1335    10.296    10.084
M. chain angle B values: others                1336    10.295    10.093
S. chain bond B values: refined atoms          1209     9.619     7.593
S. chain bond B values: others                 1207     9.622     7.587
S. chain angle B values: refined atoms         1719    13.091    11.031
S. chain angle B values: others                1719    13.087    11.031
Long range B values: refined atoms             2645    15.063    77.972
Long range B values: others                    2644    15.071    77.995
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4890, B  =   -0.0853
Partial structure    1: scale =     0.3855, B  =   54.9341
Overall anisotropic scale factors
   B11 =   4.82 B22 =  -1.53 B33 =  -3.29 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   10. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   271.5   268.2  0.20  0.20     153   258.6   252.3  0.29  0.29
 0.083    5552  99.88   134.5   123.3  0.21  0.19     305   134.0   124.2  0.28  0.26
 0.139    7124  99.77    44.8    46.0  0.28  0.24     364    46.5    49.2  0.36  0.32
 0.194    8355  99.91    24.3    21.4  0.39  0.38     424    24.2    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.5  0.56  0.56     428    19.9     9.9  0.55  0.55
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.831    698   0.763   3240   0.816  0.938  0.9132  0.9466  0.8509  0.9299
  0.0834   4838   0.803    714   0.709   5552   0.791  0.995  0.9021  0.9267  0.8554  0.9326
  0.1387   6411   0.683    713   0.633   7124   0.678  0.805  0.8250  0.8501  0.7180  0.8730
  0.1940   7643   0.317    712   0.285   8355   0.314  0.421  0.4787  0.4684  0.7033  0.7070
  0.2493   7833   0.300    643   0.289   8476   0.299  0.679  0.3294  0.3104  0.4120  0.4661
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2542
Free R factor                        =     0.3267
Average Fourier shell correlation    =     0.6356
AverageFree Fourier shell correlation=     0.6327
Overall weighted R factor            =     0.2201
Free weighted R factor               =     0.2951
Overall weighted R2 factor           =     0.2276
Free weighted R2 factor              =     0.3154
Average correlation coefficient      =     0.7411
Overall correlation coefficient      =     0.9620
Free correlation coefficient         =     0.9208
Cruickshanks DPI for coordinate error=     0.1544
DPI based on free R factor           =     0.1684
Overall figure of merit              =     0.5200
ML based su of positional parameters =     0.2690
ML based su of thermal parameters    =    11.3592
-----------------------------------------------------------------------------
 Trying gamma equal   1.90749019E-02
 Gamma decreased to   1.43992268E-02


 fvalues    131581.08       13116.404       2942738.5       2942451.0    
 fvalues    131581.08       13116.404       2942738.5       2942962.5    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset 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: poli_webinar_R00_1-90A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.014     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     2.069     1.648
Bond angles  : others                          5121     1.419     1.582
Torsion angles, period  1. refined              265     7.903     5.000
Torsion angles, period  2. refined              135    33.062    22.370
Torsion angles, period  3. refined              475    21.444    15.000
Torsion angles, period  4. refined               19    19.839    15.000
Chiral centres: refined atoms                   284     0.090     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   552     0.243     0.200
VDW repulsions.others                          2113     0.200     0.200
VDW; torsion: refined_atoms                    1105     0.176     0.200
VDW; torsion.others                            1137     0.093     0.200
HBOND: refined_atoms                             63     0.203     0.200
HBOND.others                                      1     0.327     0.200
VDW repulsions: symmetry: refined_atoms           9     0.236     0.200
VDW repulsions: symmetry: others                 39     0.213     0.200
HBOND: symmetry: refined_atoms                    2     0.130     0.200
M. chain bond B values: refined atoms          1075     8.180     6.762
M. chain bond B values: others                 1074     8.174     6.754
M. chain angle B values: refined atoms         1335    10.300    10.086
M. chain angle B values: others                1336    10.299    10.094
S. chain bond B values: refined atoms          1209     9.636     7.595
S. chain bond B values: others                 1207     9.638     7.588
S. chain angle B values: refined atoms         1719    13.104    11.032
S. chain angle B values: others                1719    13.100    11.032
Long range B values: refined atoms             2642    15.073    77.824
Long range B values: others                    2641    15.082    77.846
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4883, B  =   -0.1324
Partial structure    1: scale =     0.3853, B  =   54.7882
Overall anisotropic scale factors
   B11 =   4.81 B22 =  -1.52 B33 =  -3.29 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   11. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   271.6   268.3  0.20  0.20     153   258.8   252.3  0.28  0.29
 0.083    5552  99.88   134.6   123.4  0.20  0.19     305   134.0   124.3  0.28  0.26
 0.139    7124  99.77    44.8    46.1  0.28  0.24     364    46.5    49.3  0.36  0.33
 0.194    8355  99.91    24.3    21.5  0.39  0.38     424    24.2    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.6  0.56  0.56     428    19.9     9.9  0.55  0.55
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.831    698   0.764   3240   0.817  0.938  0.9138  0.9468  0.8517  0.9298
  0.0834   4838   0.803    714   0.709   5552   0.791  0.995  0.9020  0.9267  0.8553  0.9326
  0.1387   6411   0.683    713   0.633   7124   0.678  0.805  0.8249  0.8501  0.7167  0.8730
  0.1940   7643   0.320    712   0.288   8355   0.317  0.424  0.4807  0.4706  0.7019  0.7069
  0.2493   7833   0.301    643   0.290   8476   0.300  0.679  0.3303  0.3112  0.4130  0.4660
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2542
Free R factor                        =     0.3267
Average Fourier shell correlation    =     0.6364
AverageFree Fourier shell correlation=     0.6334
Overall weighted R factor            =     0.2200
Free weighted R factor               =     0.2949
Overall weighted R2 factor           =     0.2275
Free weighted R2 factor              =     0.3149
Average correlation coefficient      =     0.7410
Overall correlation coefficient      =     0.9620
Free correlation coefficient         =     0.9210
Cruickshanks DPI for coordinate error=     0.1543
DPI based on free R factor           =     0.1684
Overall figure of merit              =     0.5209
ML based su of positional parameters =     0.2690
ML based su of thermal parameters    =    11.3592
-----------------------------------------------------------------------------
  Time in seconds: CPU =        35.44
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2548   0.3266   0.536      131850.    6879.0   0.0131  0.908   1.983  1.177   0.087
       1   0.2548   0.3253   0.537      131586.    6874.9   0.0133  0.927   1.995  1.184   0.088
       2   0.2549   0.3262   0.545      131592.    6876.3   0.0134  0.926   2.013  1.193   0.088
       3   0.2549   0.3253   0.520      131652.    6877.9   0.0132  0.915   2.007  1.189   0.088
       4   0.2544   0.3263   0.521      131628.    6879.1   0.0139  0.962   2.048  1.214   0.089
       5   0.2543   0.3262   0.521      131608.    6878.5   0.0138  0.951   2.050  1.215   0.089
       6   0.2542   0.3265   0.519      131610.    6879.4   0.0139  0.957   2.058  1.219   0.089
       7   0.2541   0.3269   0.521      131584.    6878.7   0.0139  0.960   2.062  1.222   0.090
       8   0.2542   0.3272   0.520      131597.    6879.5   0.0138  0.956   2.063  1.222   0.089
       9   0.2542   0.3267   0.520      131583.    6879.1   0.0138  0.957   2.065  1.223   0.090
      10   0.2542   0.3267   0.521      131593.    6879.9   0.0139  0.958   2.069  1.225   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2548   0.2542
             R free    0.3266   0.3267
     Rms BondLength    0.0131   0.0139
      Rms BondAngle    1.9832   2.0685
     Rms ChirVolume    0.0875   0.0897
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      68.5s System:    0.2s Elapsed:     1:09  
</pre>
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