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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 28/ 5/2020 Run time: 10:54:33 


 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 2.30     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- ncyc 10
  Data line--- bins 5
  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_R.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - poli67_edit12_refmac1.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli67_R00_2-30A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli67_R00_2-30A.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       0.0378
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.3000
  Estimated number of reflections :      26754
  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  2.3000

  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 :poli67_edit12_refmac1.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        979
Number of   all  reflections      20219
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          20219

   Current auto weighting coefficient =    8.2496777    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :    96  132  160
 Maximuum H,K,L                 :    26   35   42
 Minimum acceptable grid spacing:    64   88  104
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :    96  132  160
 Maximuum H,K,L                 :    26   35   42
 Minimum acceptable grid spacing:    64   88  104
 Weight matrix   6.00000024E-02
 Actual weight    18.573778      is applied to the X-ray term
Norm of X_ray positional gradient                31.2
Norm of Geom. positional gradient                113.
Norm of X_ray B-factor gradient                  41.3
Norm of Geom. B-factor gradient                  19.3
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.294
Product of X_ray and Geom B-fact gradients     -0.333E+07
 Cosine of angle between them                      -0.932


Residuals: XRAY=     0.1599E+07 GEOM=     0.1719E+05 TOTAL=     0.1616E+07
 function value    1616480.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.017     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.997     1.648
Bond angles  : others                          5121     2.247     1.582
Torsion angles, period  1. refined              265     6.550     5.000
Torsion angles, period  2. refined              135    33.059    22.370
Torsion angles, period  3. refined              475    19.302    15.000
Torsion angles, period  4. refined               19    18.944    15.000
Chiral centres: refined atoms                   284     0.141     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.010     0.020
VDW repulsions: refined_atoms                   499     0.213     0.200
VDW repulsions.others                          1905     0.191     0.200
VDW; torsion: refined_atoms                    1071     0.174     0.200
VDW; torsion.others                            1143     0.077     0.200
HBOND: refined_atoms                             44     0.158     0.200
VDW repulsions: symmetry: refined_atoms          11     0.183     0.200
VDW repulsions: symmetry: others                 23     0.277     0.200
HBOND: symmetry: refined_atoms                    3     0.116     0.200
M. chain bond B values: refined atoms          1075     5.601     7.097
M. chain bond B values: others                 1074     5.583     7.088
M. chain angle B values: refined atoms         1335     8.154    10.589
M. chain angle B values: others                1336     8.155    10.598
S. chain bond B values: refined atoms          1209     6.266     7.849
S. chain bond B values: others                 1207     6.266     7.840
S. chain angle B values: refined atoms         1719     9.712    11.469
S. chain angle B values: others                1719     9.709    11.470
Long range B values: refined atoms             2570    12.299    79.861
Long range B values: others                    2569    12.302    79.835
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4908, B  =   -0.0952
Partial structure    1: scale =     0.3738, B  =   50.7439
Overall anisotropic scale factors
   B11 =   6.10 B22 =  -2.07 B33 =  -4.03 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.019    1863  99.29   294.8   290.1  0.22  0.23      98   267.4   269.4  0.31  0.32
 0.057    3175  99.79   209.9   204.4  0.19  0.18     152   214.8   203.4  0.24  0.24
 0.095    4037  99.95   106.1    94.0  0.22  0.21     233    98.8    91.8  0.31  0.28
 0.132    4727  99.70    48.4    47.1  0.27  0.23     252    49.2    49.8  0.33  0.30
 0.170    5392  99.89    29.8    27.5  0.36  0.33     243    30.6    29.2  0.40  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0193   1392   0.814    471   0.750   1863   0.798  0.916  0.9160  0.9419  0.8691  0.9187
  0.0570   2695   0.835    480   0.744   3175   0.822  0.963  0.9228  0.9388  0.8464  0.9217
  0.0947   3547   0.802    490   0.711   4037   0.791  1.023  0.8824  0.9200  0.7814  0.9201
  0.1325   4243   0.708    484   0.657   4727   0.703  0.880  0.8330  0.8512  0.7236  0.8702
  0.1702   4903   0.489    492   0.439   5395   0.484  0.672  0.6083  0.6181  0.6998  0.7797
 $$
Resolution limits                    =     47.324     2.300
Number of used reflections           =      19196
Percentage observed                  =    99.7725
Percentage of free reflections       =     4.8478
Overall R factor                     =     0.2266
Free R factor                        =     0.2962
Average Fourier shell correlation    =     0.8234
AverageFree Fourier shell correlation=     0.8112
Overall weighted R factor            =     0.2105
Free weighted R factor               =     0.2802
Overall weighted R2 factor           =     0.2356
Free weighted R2 factor              =     0.3108
Average correlation coefficient      =     0.8685
Overall correlation coefficient      =     0.9529
Free correlation coefficient         =     0.9136
Cruickshanks DPI for coordinate error=     0.2529
DPI based on free R factor           =     0.2392
Overall figure of merit              =     0.6887
ML based su of positional parameters =     0.2459
ML based su of thermal parameters    =    11.0191
-----------------------------------------------------------------------------
 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    86104.680       17191.539       1616480.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   6.00000024E-02
 Actual weight    18.502314      is applied to the X-ray term


 function value    1601978.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4889, B  =   -0.1616
Partial structure    1: scale =     0.3738, B  =   50.8923
Overall anisotropic scale factors
   B11 =   6.09 B22 =  -2.08 B33 =  -4.02 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2252
Free R factor                        =     0.2971
Average Fourier shell correlation    =     0.8172
AverageFree Fourier shell correlation=     0.8043
Average correlation coefficient      =     0.8721
Overall figure of merit              =     0.6783
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    86024.063       10334.645       1601978.8       1616480.8    


     CGMAT cycle number =      3

 Weight matrix   5.99999987E-02
 Actual weight    17.618265      is applied to the X-ray term


 function value    1523749.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4882, B  =   -0.0366
Partial structure    1: scale =     0.3733, B  =   50.8050
Overall anisotropic scale factors
   B11 =   6.09 B22 =  -2.08 B33 =  -4.00 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2242
Free R factor                        =     0.2977
Average Fourier shell correlation    =     0.8267
AverageFree Fourier shell correlation=     0.8132
Average correlation coefficient      =     0.8720
Overall figure of merit              =     0.6955
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    85885.383       10597.857       1523749.4       1601978.8    


     CGMAT cycle number =      4

 Weight matrix   5.99999987E-02
 Actual weight    18.257231      is applied to the X-ray term


 function value    1580915.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4855, B  =   -0.1578
Partial structure    1: scale =     0.3726, B  =   50.7768
Overall anisotropic scale factors
   B11 =   6.07 B22 =  -2.09 B33 =  -3.98 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2240
Free R factor                        =     0.2974
Average Fourier shell correlation    =     0.8195
AverageFree Fourier shell correlation=     0.8061
Average correlation coefficient      =     0.8728
Overall figure of merit              =     0.6820
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02


 fvalues    85928.141       10550.118       1581111.8       1523749.4    

 fvalues    85928.141       10550.118       1581279.8       1579360.0    
 fvalues    85928.141       10550.118       1581279.8       1579360.0    


     CGMAT cycle number =      5

 Weight matrix   5.99999987E-02
 Actual weight    18.404970      is applied to the X-ray term


 function value    1594140.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4843, B  =   -0.1094
Partial structure    1: scale =     0.3723, B  =   50.7752
Overall anisotropic scale factors
   B11 =   6.08 B22 =  -2.09 B33 =  -3.98 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2239
Free R factor                        =     0.2975
Average Fourier shell correlation    =     0.8185
AverageFree Fourier shell correlation=     0.8051
Average correlation coefficient      =     0.8728
Overall figure of merit              =     0.6804
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    85934.227       10606.473       1594105.0       1579360.0    

 fvalues    85934.227       10606.473       1594101.8       1592223.4    
 fvalues    85934.227       10606.473       1594101.8       1592223.4    


     CGMAT cycle number =      6

 Weight matrix   6.00000024E-02
 Actual weight    18.358027      is applied to the X-ray term


 function value    1589754.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4855, B  =   -0.1083
Partial structure    1: scale =     0.3725, B  =   50.6823
Overall anisotropic scale factors
   B11 =   6.08 B22 =  -2.10 B33 =  -3.99 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2238
Free R factor                        =     0.2974
Average Fourier shell correlation    =     0.8185
AverageFree Fourier shell correlation=     0.8051
Average correlation coefficient      =     0.8727
Overall figure of merit              =     0.6803
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03
 fvalues    86018.297       10628.111       1589754.3       1592223.4    


     CGMAT cycle number =      7

 Weight matrix   5.99999987E-02
 Actual weight    17.739756      is applied to the X-ray term


 function value    1535026.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4845, B  =   -0.1177
Partial structure    1: scale =     0.3726, B  =   50.6678
Overall anisotropic scale factors
   B11 =   6.08 B22 =  -2.10 B33 =  -3.99 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2237
Free R factor                        =     0.2973
Average Fourier shell correlation    =     0.8261
AverageFree Fourier shell correlation=     0.8122
Average correlation coefficient      =     0.8727
Overall figure of merit              =     0.6938
-----------------------------------------------------------------------------
 Trying gamma equal   2.19674082E-03
 Not converging with gamma equal   2.19674082E-03
 Trying gamma equal   3.33133601E-02
 Gamma decreased to   2.70900354E-02
 fvalues    85929.313       10660.974       1535026.0       1589754.3    


     CGMAT cycle number =      8

 Weight matrix   6.00000024E-02
 Actual weight    18.424612      is applied to the X-ray term


 function value    1595851.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4841, B  =   -0.0883
Partial structure    1: scale =     0.3728, B  =   50.6953
Overall anisotropic scale factors
   B11 =   6.08 B22 =  -2.10 B33 =  -3.98 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2236
Free R factor                        =     0.2971
Average Fourier shell correlation    =     0.8183
AverageFree Fourier shell correlation=     0.8048
Average correlation coefficient      =     0.8728
Overall figure of merit              =     0.6799
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02


 fvalues    85931.492       10664.887       1595785.3       1535026.0    

 fvalues    85931.492       10664.887       1595766.5       1593919.3    
 fvalues    85931.492       10664.887       1595766.5       1593919.3    


     CGMAT cycle number =      9

 Weight matrix   5.99999987E-02
 Actual weight    18.344038      is applied to the X-ray term


 function value    1588808.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4842, B  =   -0.1411
Partial structure    1: scale =     0.3732, B  =   50.7288
Overall anisotropic scale factors
   B11 =   6.08 B22 =  -2.10 B33 =  -3.98 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2236
Free R factor                        =     0.2971
Average Fourier shell correlation    =     0.8187
AverageFree Fourier shell correlation=     0.8051
Average correlation coefficient      =     0.8728
Overall figure of merit              =     0.6805
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02
 fvalues    86029.898       10672.513       1588808.3       1593919.3    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :    96  132  160
 Maximuum H,K,L                 :    26   35   42
 Minimum acceptable grid spacing:    64   88  104
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :    96  132  160
 Maximuum H,K,L                 :    26   35   42
 Minimum acceptable grid spacing:    64   88  104
 Weight matrix   5.99999987E-02
 Actual weight    17.727859      is applied to the X-ray term
Norm of X_ray positional gradient                28.3
Norm of Geom. positional gradient                28.5
Norm of X_ray B-factor gradient                  30.4
Norm of Geom. B-factor gradient                  29.5
Product of X_ray and Geom posit. gradients     -0.108E+08
 Cosine of angle between them                      -0.996
Product of X_ray and Geom B-fact gradients     -0.398E+07
 Cosine of angle between them                      -0.990


Residuals: XRAY=     0.1524E+07 GEOM=     0.1068E+05 TOTAL=     0.1534E+07
 function value    1534302.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.829     1.648
Bond angles  : others                          5121     1.376     1.582
Torsion angles, period  1. refined              265     7.299     5.000
Torsion angles, period  2. refined              135    32.822    22.370
Torsion angles, period  3. refined              475    19.922    15.000
Torsion angles, period  4. refined               19    19.826    15.000
Chiral centres: refined atoms                   284     0.081     0.200
Planar groups: refined atoms                   2462     0.009     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   502     0.224     0.200
VDW repulsions.others                          1945     0.190     0.200
VDW; torsion: refined_atoms                    1094     0.170     0.200
VDW; torsion.others                            1069     0.090     0.200
HBOND: refined_atoms                             50     0.179     0.200
VDW repulsions: symmetry: refined_atoms          10     0.198     0.200
VDW repulsions: symmetry: others                 28     0.245     0.200
HBOND: symmetry: refined_atoms                    2     0.147     0.200
M. chain bond B values: refined atoms          1075     7.526     7.057
M. chain bond B values: others                 1074     7.504     7.046
M. chain angle B values: refined atoms         1335    10.022    10.524
M. chain angle B values: others                1336    10.026    10.534
S. chain bond B values: refined atoms          1209     8.790     7.903
S. chain bond B values: others                 1207     8.790     7.894
S. chain angle B values: refined atoms         1719    12.514    11.492
S. chain angle B values: others                1719    12.509    11.492
Long range B values: refined atoms             2583    14.722    79.730
Long range B values: others                    2583    14.731    79.779
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4831, B  =   -0.1477
Partial structure    1: scale =     0.3733, B  =   50.7897
Overall anisotropic scale factors
   B11 =   6.07 B22 =  -2.10 B33 =  -3.98 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.019    1863  99.29   296.3   290.5  0.22  0.23      98   268.8   269.8  0.31  0.32
 0.057    3175  99.79   211.0   205.2  0.18  0.18     152   215.9   203.7  0.24  0.24
 0.095    4037  99.95   106.6    94.1  0.22  0.20     233    99.3    91.8  0.31  0.28
 0.132    4727  99.70    48.6    47.4  0.26  0.22     252    49.4    50.2  0.34  0.31
 0.170    5392  99.89    30.0    28.1  0.36  0.33     243    30.8    29.6  0.40  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0193   1392   0.824    471   0.759   1863   0.808  0.919  0.9184  0.9435  0.8693  0.9190
  0.0570   2695   0.838    480   0.748   3175   0.824  0.964  0.9236  0.9414  0.8450  0.9253
  0.0947   3547   0.803    490   0.713   4037   0.792  1.023  0.8831  0.9220  0.7855  0.9252
  0.1325   4243   0.717    484   0.667   4727   0.712  0.886  0.8365  0.8580  0.7171  0.8768
  0.1702   4903   0.494    492   0.444   5395   0.489  0.676  0.6074  0.6188  0.6918  0.7830
 $$
Resolution limits                    =     47.324     2.300
Number of used reflections           =      19196
Percentage observed                  =    99.7725
Percentage of free reflections       =     4.8478
Overall R factor                     =     0.2236
Free R factor                        =     0.2972
Average Fourier shell correlation    =     0.8263
AverageFree Fourier shell correlation=     0.8124
Overall weighted R factor            =     0.2079
Free weighted R factor               =     0.2814
Overall weighted R2 factor           =     0.2330
Free weighted R2 factor              =     0.3117
Average correlation coefficient      =     0.8728
Overall correlation coefficient      =     0.9539
Free correlation coefficient         =     0.9134
Cruickshanks DPI for coordinate error=     0.2495
DPI based on free R factor           =     0.2400
Overall figure of merit              =     0.6940
ML based su of positional parameters =     0.2400
ML based su of thermal parameters    =    10.7669
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02
 fvalues    85944.836       10684.230       1534302.3       1588808.3    

 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: poli67_R00_2-30A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.829     1.648
Bond angles  : others                          5121     1.376     1.582
Torsion angles, period  1. refined              265     7.303     5.000
Torsion angles, period  2. refined              135    32.825    22.370
Torsion angles, period  3. refined              475    19.931    15.000
Torsion angles, period  4. refined               19    19.836    15.000
Chiral centres: refined atoms                   284     0.081     0.200
Planar groups: refined atoms                   2462     0.009     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   503     0.224     0.200
VDW repulsions.others                          1943     0.190     0.200
VDW; torsion: refined_atoms                    1095     0.170     0.200
VDW; torsion.others                            1069     0.090     0.200
HBOND: refined_atoms                             50     0.179     0.200
VDW repulsions: symmetry: refined_atoms          10     0.199     0.200
VDW repulsions: symmetry: others                 28     0.245     0.200
HBOND: symmetry: refined_atoms                    2     0.147     0.200
M. chain bond B values: refined atoms          1075     7.527     7.055
M. chain bond B values: others                 1074     7.505     7.045
M. chain angle B values: refined atoms         1335    10.021    10.523
M. chain angle B values: others                1336    10.025    10.532
S. chain bond B values: refined atoms          1209     8.789     7.902
S. chain bond B values: others                 1207     8.789     7.893
S. chain angle B values: refined atoms         1719    12.514    11.490
S. chain angle B values: others                1719    12.509    11.490
Long range B values: refined atoms             2585    14.727    79.776
Long range B values: others                    2585    14.736    79.825
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4829, B  =   -0.1576
Partial structure    1: scale =     0.3731, B  =   50.7355
Overall anisotropic scale factors
   B11 =   6.07 B22 =  -2.10 B33 =  -3.97 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.019    1863  99.29   296.4   290.5  0.22  0.23      98   268.8   269.8  0.31  0.32
 0.057    3175  99.79   211.0   205.3  0.18  0.18     152   215.9   203.8  0.24  0.24
 0.095    4037  99.95   106.7    94.1  0.22  0.20     233    99.3    91.8  0.31  0.28
 0.132    4727  99.70    48.6    47.4  0.26  0.22     252    49.4    50.2  0.34  0.31
 0.170    5392  99.89    30.0    28.1  0.36  0.33     243    30.8    29.6  0.40  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0193   1392   0.824    471   0.759   1863   0.808  0.919  0.9185  0.9435  0.8694  0.9191
  0.0570   2695   0.838    480   0.748   3175   0.824  0.964  0.9236  0.9414  0.8451  0.9253
  0.0947   3547   0.803    490   0.713   4037   0.792  1.023  0.8832  0.9220  0.7856  0.9252
  0.1325   4243   0.717    484   0.667   4727   0.712  0.886  0.8365  0.8581  0.7169  0.8768
  0.1702   4903   0.445    492   0.400   5395   0.441  0.626  0.5782  0.5919  0.6918  0.7831
 $$
Resolution limits                    =     47.324     2.300
Number of used reflections           =      19196
Percentage observed                  =    99.7725
Percentage of free reflections       =     4.8478
Overall R factor                     =     0.2236
Free R factor                        =     0.2971
Average Fourier shell correlation    =     0.8188
AverageFree Fourier shell correlation=     0.8052
Overall weighted R factor            =     0.2079
Free weighted R factor               =     0.2813
Overall weighted R2 factor           =     0.2330
Free weighted R2 factor              =     0.3116
Average correlation coefficient      =     0.8728
Overall correlation coefficient      =     0.9539
Free correlation coefficient         =     0.9134
Cruickshanks DPI for coordinate error=     0.2495
DPI based on free R factor           =     0.2400
Overall figure of merit              =     0.6805
ML based su of positional parameters =     0.2400
ML based su of thermal parameters    =    10.7669
-----------------------------------------------------------------------------
  Time in seconds: CPU =        24.05
             Elapsed =           0.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2266   0.2962   0.689       86105.    4519.9   0.0168  1.426   1.997  1.251   0.141
       1   0.2252   0.2971   0.678       86024.    4524.7   0.0124  0.881   1.767  1.067   0.082
       2   0.2242   0.2977   0.695       85885.    4521.1   0.0121  0.849   1.810  1.085   0.080
       3   0.2240   0.2974   0.682       86013.    4527.3   0.0117  0.816   1.814  1.082   0.080
       4   0.2239   0.2975   0.680       86038.    4528.2   0.0117  0.818   1.819  1.085   0.080
       5   0.2238   0.2974   0.680       86018.    4527.7   0.0117  0.819   1.822  1.086   0.080
       6   0.2237   0.2973   0.694       85929.    4524.4   0.0117  0.820   1.826  1.088   0.081
       7   0.2236   0.2971   0.680       86036.    4528.7   0.0117  0.819   1.827  1.088   0.081
       8   0.2236   0.2971   0.680       86030.    4528.9   0.0117  0.819   1.827  1.088   0.081
       9   0.2236   0.2972   0.694       85945.    4525.7   0.0117  0.819   1.829  1.089   0.081
      10   0.2236   0.2971   0.680       86048.    4529.9   0.0117  0.819   1.829  1.089   0.081
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2266   0.2236
             R free    0.2962   0.2971
     Rms BondLength    0.0168   0.0117
      Rms BondAngle    1.9973   1.8290
     Rms ChirVolume    0.1409   0.0808
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      65.3s System:    0.2s Elapsed:     1:06  
</pre>
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