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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 28/ 5/2020 Run time: 11:07:23 


 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_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_R00_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli67_R00_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli67_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 :poli67_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    22.544830      is applied to the X-ray term
Norm of X_ray positional gradient                35.2
Norm of Geom. positional gradient                78.0
Norm of X_ray B-factor gradient                  36.3
Norm of Geom. B-factor gradient                  33.2
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.382
Product of X_ray and Geom B-fact gradients     -0.427E+07
 Cosine of angle between them                      -0.791


Residuals: XRAY=     0.2973E+07 GEOM=     0.1906E+05 TOTAL=     0.2992E+07
 function value    2991587.8    

-------------------------------------------------------------------------------
             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     2.005     1.648
Bond angles  : others                          5121     2.294     1.582
Torsion angles, period  1. refined              265     7.849     5.000
Torsion angles, period  2. refined              135    33.021    22.370
Torsion angles, period  3. refined              475    21.247    15.000
Torsion angles, period  4. refined               19    20.368    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.015     0.020
VDW repulsions: refined_atoms                   554     0.240     0.200
VDW repulsions.others                          2004     0.232     0.200
VDW; torsion: refined_atoms                    1099     0.176     0.200
VDW; torsion.others                            1055     0.084     0.200
HBOND: refined_atoms                             59     0.204     0.200
HBOND.others                                      2     0.041     0.200
VDW repulsions: symmetry: refined_atoms          10     0.235     0.200
VDW repulsions: symmetry: others                 33     0.242     0.200
HBOND: symmetry: refined_atoms                    2     0.123     0.200
M. chain bond B values: refined atoms          1075     7.957     6.846
M. chain bond B values: others                 1074     7.949     6.838
M. chain angle B values: refined atoms         1335    10.125    10.214
M. chain angle B values: others                1336    10.123    10.222
S. chain bond B values: refined atoms          1209     9.379     7.680
S. chain bond B values: others                 1207     9.380     7.673
S. chain angle B values: refined atoms         1719    12.929    11.164
S. chain angle B values: others                1719    12.924    11.164
Long range B values: refined atoms             2633    14.901    78.771
Long range B values: others                    2632    14.914    78.791
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4868, B  =   -1.0430
Partial structure    1: scale =     0.3840, B  =   55.8626
Overall anisotropic scale factors
   B11 =   4.83 B22 =  -1.48 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   271.9   268.6  0.20  0.20     153   259.0   252.7  0.28  0.28
 0.083    5552  99.88   134.7   123.3  0.20  0.19     305   134.2   124.2  0.28  0.26
 0.139    7124  99.77    44.9    46.1  0.28  0.24     364    46.5    49.3  0.36  0.32
 0.194    8355  99.91    24.3    21.6  0.39  0.38     424    24.2    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.6  0.56  0.56     428    20.0    10.0  0.55  0.55
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.823    698   0.755   3240   0.809  0.935  0.9134  0.9453  0.8549  0.9287
  0.0834   4838   0.800    714   0.707   5552   0.788  0.996  0.9030  0.9279  0.8570  0.9348
  0.1387   6411   0.657    713   0.609   7124   0.652  0.792  0.8092  0.8339  0.7187  0.8711
  0.1940   7643   0.409    712   0.358   8355   0.405  0.553  0.5180  0.5140  0.7058  0.7087
  0.2493   7833   0.309    643   0.302   8476   0.308  0.694  0.3353  0.3145  0.4147  0.4683
 $$
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                        =     0.3257
Average Fourier shell correlation    =     0.6448
AverageFree Fourier shell correlation=     0.6409
Overall weighted R factor            =     0.2198
Free weighted R factor               =     0.2930
Overall weighted R2 factor           =     0.2272
Free weighted R2 factor              =     0.3110
Average correlation coefficient      =     0.7419
Overall correlation coefficient      =     0.9618
Free correlation coefficient         =     0.9223
Cruickshanks DPI for coordinate error=     0.1544
DPI based on free R factor           =     0.1679
Overall figure of merit              =     0.5385
ML based su of positional parameters =     0.2709
ML based su of thermal parameters    =    11.3149
-----------------------------------------------------------------------------
 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    131849.55       19061.906       2991587.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   6.00000024E-02
 Actual weight    20.811253      is applied to the X-ray term


 function value    2750369.5    

-------------------------------------------------------------------------------
             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 =     1.4885, B  =   -0.2208
Partial structure    1: scale =     0.3857, B  =   55.3557
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.47 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2541
Free R factor                        =     0.3248
Average Fourier shell correlation    =     0.6459
AverageFree Fourier shell correlation=     0.6429
Average correlation coefficient      =     0.7424
Overall figure of merit              =     0.5404
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    131546.08       12730.674       2750369.5       2991587.8    


     CGMAT cycle number =      3

 Weight matrix   5.99999949E-02
 Actual weight    20.973202      is applied to the X-ray term


 function value    2772538.8    

-------------------------------------------------------------------------------
             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 =     1.4869, B  =   -0.1983
Partial structure    1: scale =     0.3854, B  =   55.0328
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.48 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3257
Average Fourier shell correlation    =     0.6449
AverageFree Fourier shell correlation=     0.6415
Average correlation coefficient      =     0.7420
Overall figure of merit              =     0.5391
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02


 fvalues    131605.41       12778.113       2772487.8       2750369.5    
 fvalues    131605.41       12778.113       2772487.8       2772964.8    


     CGMAT cycle number =      4

 Weight matrix   6.00000024E-02
 Actual weight    20.957199      is applied to the X-ray term


 function value    2770485.5    

-------------------------------------------------------------------------------
             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 =     1.4867, B  =   -0.1741
Partial structure    1: scale =     0.3857, B  =   54.9513
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.49 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3259
Average Fourier shell correlation    =     0.6450
AverageFree Fourier shell correlation=     0.6416
Average correlation coefficient      =     0.7419
Overall figure of merit              =     0.5391
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    131587.28       12784.706       2770485.5       2772964.8    


     CGMAT cycle number =      5

 Weight matrix   5.99999987E-02
 Actual weight    20.881516      is applied to the X-ray term


 function value    2760846.8    

-------------------------------------------------------------------------------
             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 =     1.4856, B  =   -0.2095
Partial structure    1: scale =     0.3859, B  =   54.8997
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.48 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3259
Average Fourier shell correlation    =     0.6455
AverageFree Fourier shell correlation=     0.6421
Average correlation coefficient      =     0.7419
Overall figure of merit              =     0.5396
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03
 fvalues    131602.25       12792.168       2760846.8       2770485.5    


     CGMAT cycle number =      6

 Weight matrix   5.99999987E-02
 Actual weight    20.901682      is applied to the X-ray term


 function value    2762955.0    

-------------------------------------------------------------------------------
             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 =     1.4869, B  =   -0.1627
Partial structure    1: scale =     0.3858, B  =   54.8716
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.49 B33 =  -3.29 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3259
Average Fourier shell correlation    =     0.6453
AverageFree Fourier shell correlation=     0.6419
Average correlation coefficient      =     0.7417
Overall figure of merit              =     0.5394
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    131578.97       12777.066       2762913.8       2760846.8    
 fvalues    131578.97       12777.066       2762913.8       2762998.8    


     CGMAT cycle number =      7

 Weight matrix   5.99999987E-02
 Actual weight    20.949423      is applied to the X-ray term


 function value    2769504.8    

-------------------------------------------------------------------------------
             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 =     1.4861, B  =   -0.1686
Partial structure    1: scale =     0.3859, B  =   55.1051
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.50 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2545
Free R factor                        =     0.3259
Average Fourier shell correlation    =     0.6449
AverageFree Fourier shell correlation=     0.6416
Average correlation coefficient      =     0.7419
Overall figure of merit              =     0.5390
-----------------------------------------------------------------------------
 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    131593.53       12778.516       2769705.8       2762998.8    

 fvalues    131593.53       12778.516       2769580.3       2769587.0    
 fvalues    131593.53       12778.516       2769580.3       2769587.0    


     CGMAT cycle number =      8

 Weight matrix   5.99999912E-02
 Actual weight    20.959911      is applied to the X-ray term


 function value    2771125.5    

-------------------------------------------------------------------------------
             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 =     1.4855, B  =   -0.1795
Partial structure    1: scale =     0.3859, B  =   55.0859
Overall anisotropic scale factors
   B11 =   4.80 B22 =  -1.50 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3259
Average Fourier shell correlation    =     0.6447
AverageFree Fourier shell correlation=     0.6413
Average correlation coefficient      =     0.7419
Overall figure of merit              =     0.5388
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02


 fvalues    131607.05       12777.457       2771338.3       2769587.0    

 fvalues    131607.05       12777.457       2771326.0       2771249.5    
 fvalues    131607.05       12777.457       2771326.0       2771249.5    


     CGMAT cycle number =      9

 Weight matrix   5.99999949E-02
 Actual weight    20.875320      is applied to the X-ray term


 function value    2760436.8    

-------------------------------------------------------------------------------
             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 =     1.4847, B  =   -0.1965
Partial structure    1: scale =     0.3859, B  =   55.1261
Overall anisotropic scale factors
   B11 =   4.80 B22 =  -1.50 B33 =  -3.29 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3261
Average Fourier shell correlation    =     0.6454
AverageFree Fourier shell correlation=     0.6421
Average correlation coefficient      =     0.7418
Overall figure of merit              =     0.5397
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02
 fvalues    131622.27       12779.654       2760436.8       2771249.5    


     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    21.073143      is applied to the X-ray term
Norm of X_ray positional gradient                34.8
Norm of Geom. positional gradient                34.5
Norm of X_ray B-factor gradient                  35.3
Norm of Geom. B-factor gradient                  35.9
Product of X_ray and Geom posit. gradients     -0.161E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.567E+07
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.2774E+07 GEOM=     0.1277E+05 TOTAL=     0.2787E+07
 function value    2786572.3    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   3054     2.039     1.648
Bond angles  : others                          5121     1.409     1.582
Torsion angles, period  1. refined              265     7.943     5.000
Torsion angles, period  2. refined              135    33.079    22.370
Torsion angles, period  3. refined              475    21.549    15.000
Torsion angles, period  4. refined               19    19.804    15.000
Chiral centres: refined atoms                   284     0.089     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   558     0.242     0.200
VDW repulsions.others                          2073     0.202     0.200
VDW; torsion: refined_atoms                    1102     0.176     0.200
VDW; torsion.others                            1135     0.093     0.200
HBOND: refined_atoms                             58     0.219     0.200
HBOND.others                                      1     0.323     0.200
VDW repulsions: symmetry: refined_atoms           9     0.242     0.200
VDW repulsions: symmetry: others                 37     0.217     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     7.966     6.753
M. chain bond B values: others                 1074     7.966     6.746
M. chain angle B values: refined atoms         1335    10.121    10.076
M. chain angle B values: others                1336    10.119    10.084
S. chain bond B values: refined atoms          1209     9.396     7.582
S. chain bond B values: others                 1207     9.399     7.576
S. chain angle B values: refined atoms         1719    12.861    11.018
S. chain angle B values: others                1719    12.859    11.019
Long range B values: refined atoms             2638    14.980    77.845
Long range B values: others                    2637    14.988    77.865
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4844, B  =   -0.1697
Partial structure    1: scale =     0.3861, B  =   55.2556
Overall anisotropic scale factors
   B11 =   4.80 B22 =  -1.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   272.3   268.4  0.20  0.20     153   259.4   252.7  0.29  0.29
 0.083    5552  99.88   134.9   123.6  0.21  0.19     305   134.4   124.8  0.28  0.26
 0.139    7124  99.77    44.9    46.1  0.28  0.24     364    46.6    49.4  0.36  0.32
 0.194    8355  99.91    24.4    21.5  0.39  0.38     424    24.3    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.6  0.56  0.56     428    20.0    10.0  0.55  0.55
$$

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

 $TABLE: Cycle   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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.832    698   0.763   3240   0.817  0.938  0.9132  0.9469  0.8507  0.9295
  0.0834   4838   0.805    714   0.710   5552   0.792  0.996  0.9044  0.9279  0.8585  0.9325
  0.1387   6411   0.686    713   0.636   7124   0.681  0.807  0.8272  0.8508  0.7191  0.8722
  0.1940   7643   0.377    712   0.331   8355   0.373  0.518  0.4999  0.4935  0.7044  0.7103
  0.2493   7833   0.308    643   0.298   8476   0.307  0.693  0.3359  0.3167  0.4132  0.4668
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2544
Free R factor                        =     0.3260
Average Fourier shell correlation    =     0.6440
AverageFree Fourier shell correlation=     0.6406
Overall weighted R factor            =     0.2202
Free weighted R factor               =     0.2930
Overall weighted R2 factor           =     0.2279
Free weighted R2 factor              =     0.3124
Average correlation coefficient      =     0.7419
Overall correlation coefficient      =     0.9618
Free correlation coefficient         =     0.9213
Cruickshanks DPI for coordinate error=     0.1545
DPI based on free R factor           =     0.1681
Overall figure of merit              =     0.5379
ML based su of positional parameters =     0.2617
ML based su of thermal parameters    =    10.9907
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    131614.50       12774.893       2786501.0       2760436.8    

 fvalues    131614.50       12774.893       2786556.5       2786306.3    
 fvalues    131614.50       12774.893       2786556.5       2786306.3    

 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_1-90A.mtz 


-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   3054     2.040     1.648
Bond angles  : others                          5121     1.409     1.582
Torsion angles, period  1. refined              265     7.944     5.000
Torsion angles, period  2. refined              135    33.079    22.370
Torsion angles, period  3. refined              475    21.550    15.000
Torsion angles, period  4. refined               19    19.801    15.000
Chiral centres: refined atoms                   284     0.089     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   558     0.242     0.200
VDW repulsions.others                          2072     0.202     0.200
VDW; torsion: refined_atoms                    1102     0.176     0.200
VDW; torsion.others                            1136     0.093     0.200
HBOND: refined_atoms                             59     0.217     0.200
HBOND.others                                      1     0.325     0.200
VDW repulsions: symmetry: refined_atoms           9     0.242     0.200
VDW repulsions: symmetry: others                 37     0.217     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     7.967     6.753
M. chain bond B values: others                 1074     7.968     6.745
M. chain angle B values: refined atoms         1335    10.123    10.075
M. chain angle B values: others                1336    10.121    10.083
S. chain bond B values: refined atoms          1209     9.398     7.582
S. chain bond B values: others                 1207     9.401     7.576
S. chain angle B values: refined atoms         1719    12.863    11.017
S. chain angle B values: others                1719    12.861    11.018
Long range B values: refined atoms             2639    14.980    77.859
Long range B values: others                    2638    14.987    77.878
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4842, B  =   -0.1834
Partial structure    1: scale =     0.3860, B  =   55.3683
Overall anisotropic scale factors
   B11 =   4.80 B22 =  -1.51 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   272.3   268.4  0.20  0.20     153   259.5   252.8  0.29  0.29
 0.083    5552  99.88   135.0   123.6  0.21  0.19     305   134.4   124.8  0.28  0.26
 0.139    7124  99.77    44.9    46.1  0.28  0.24     364    46.6    49.5  0.36  0.32
 0.194    8355  99.91    24.4    21.5  0.39  0.38     424    24.3    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.6  0.56  0.56     428    20.0    10.0  0.55  0.55
$$

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

 $TABLE: Cycle   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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.832    698   0.763   3240   0.817  0.938  0.9133  0.9469  0.8508  0.9294
  0.0834   4838   0.804    714   0.710   5552   0.792  0.996  0.9044  0.9279  0.8584  0.9324
  0.1387   6411   0.686    713   0.636   7124   0.681  0.807  0.8272  0.8509  0.7191  0.8722
  0.1940   7643   0.385    712   0.338   8355   0.381  0.533  0.5066  0.5002  0.7043  0.7103
  0.2493   7833   0.308    643   0.298   8476   0.307  0.693  0.3361  0.3170  0.4133  0.4669
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2544
Free R factor                        =     0.3260
Average Fourier shell correlation    =     0.6458
AverageFree Fourier shell correlation=     0.6424
Overall weighted R factor            =     0.2202
Free weighted R factor               =     0.2930
Overall weighted R2 factor           =     0.2279
Free weighted R2 factor              =     0.3124
Average correlation coefficient      =     0.7419
Overall correlation coefficient      =     0.9618
Free correlation coefficient         =     0.9213
Cruickshanks DPI for coordinate error=     0.1545
DPI based on free R factor           =     0.1681
Overall figure of merit              =     0.5401
ML based su of positional parameters =     0.2617
ML based su of thermal parameters    =    10.9907
-----------------------------------------------------------------------------
  Time in seconds: CPU =        40.99
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2542   0.3257   0.539      131850.    6880.1   0.0130  0.903   2.005  1.186   0.088
       1   0.2541   0.3248   0.540      131546.    6874.2   0.0133  0.925   2.011  1.189   0.088
       2   0.2543   0.3257   0.539      131585.    6877.7   0.0133  0.922   2.023  1.196   0.088
       3   0.2543   0.3259   0.539      131587.    6878.1   0.0134  0.927   2.029  1.200   0.088
       4   0.2544   0.3259   0.540      131602.    6878.8   0.0134  0.926   2.033  1.202   0.088
       5   0.2544   0.3259   0.539      131577.    6878.0   0.0134  0.926   2.034  1.203   0.088
       6   0.2545   0.3259   0.539      131590.    6878.5   0.0134  0.927   2.037  1.204   0.088
       7   0.2544   0.3259   0.539      131601.    6879.3   0.0134  0.927   2.039  1.205   0.089
       8   0.2544   0.3261   0.540      131622.    6880.4   0.0134  0.927   2.039  1.205   0.089
       9   0.2544   0.3260   0.538      131627.    6880.6   0.0134  0.927   2.039  1.205   0.089
      10   0.2544   0.3260   0.540      131630.    6880.6   0.0134  0.927   2.040  1.205   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2542   0.2544
             R free    0.3257   0.3260
     Rms BondLength    0.0130   0.0134
      Rms BondAngle    2.0048   2.0397
     Rms ChirVolume    0.0879   0.0886
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      75.4s System:    0.2s Elapsed:     1:16  
</pre>
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