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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: 10:55:47 


 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 2.20     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_2-30A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli67_R00_2-20A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli67_R00_2-20A.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       0.0413
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.2000
  Estimated number of reflections :      30769
  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  2.2000

  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_2-30A.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       1112
Number of   all  reflections      23041
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          23041

   Current auto weighting coefficient =    7.9996209    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   100  140  160
 Maximuum H,K,L                 :    27   37   44
 Minimum acceptable grid spacing:    66   91  107
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   100  140  160
 Maximuum H,K,L                 :    27   37   44
 Minimum acceptable grid spacing:    66   91  107
 Weight matrix   5.99999949E-02
 Actual weight    19.994282      is applied to the X-ray term
Norm of X_ray positional gradient                31.3
Norm of Geom. positional gradient                76.2
Norm of X_ray B-factor gradient                  34.2
Norm of Geom. B-factor gradient                  28.4
Product of X_ray and Geom posit. gradients     -0.112E+08
 Cosine of angle between them                      -0.349
Product of X_ray and Geom B-fact gradients     -0.373E+07
 Cosine of angle between them                      -0.856


Residuals: XRAY=     0.1917E+07 GEOM=     0.1706E+05 TOTAL=     0.1934E+07
 function value    1934360.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.829     1.648
Bond angles  : others                          5121     2.254     1.582
Torsion angles, period  1. refined              265     7.302     5.000
Torsion angles, period  2. refined              135    32.821    22.370
Torsion angles, period  3. refined              475    19.929    15.000
Torsion angles, period  4. refined               19    19.829    15.000
Chiral centres: refined atoms                   284     0.081     0.200
Planar groups: refined atoms                   2462     0.009     0.020
Planar groups: others                           467     0.013     0.020
VDW repulsions: refined_atoms                   502     0.224     0.200
VDW repulsions.others                          1903     0.216     0.200
VDW; torsion: refined_atoms                    1095     0.170     0.200
VDW; torsion.others                            1039     0.078     0.200
HBOND: refined_atoms                             50     0.179     0.200
HBOND.others                                      1     0.002     0.200
VDW repulsions: symmetry: refined_atoms          10     0.198     0.200
VDW repulsions: symmetry: others                 26     0.263     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    10.022    10.533
S. chain bond B values: refined atoms          1209     8.789     7.902
S. chain bond B values: others                 1207     8.787     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             2584    14.729    79.765
Long range B values: others                    2584    14.743    79.812
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4731, B  =   -0.6788
Partial structure    1: scale =     0.3713, B  =   52.8140
Overall anisotropic scale factors
   B11 =   5.82 B22 =  -1.93 B33 =  -3.89 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.021    2114  99.33   290.6   287.9  0.22  0.23     106   269.7   274.6  0.31  0.32
 0.062    3639  99.84   199.9   189.8  0.19  0.18     173   204.6   189.5  0.25  0.24
 0.104    4584  99.69    87.3    78.4  0.22  0.20     262    85.2    79.8  0.31  0.29
 0.145    5417  99.93    40.5    40.0  0.29  0.25     276    43.3    42.9  0.36  0.32
 0.186    6128  99.92    26.0    22.8  0.39  0.38     292    26.7    24.2  0.42  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0211   1602   0.810    512   0.746   2114   0.795  0.914  0.9182  0.9401  0.8694  0.9184
  0.0623   3107   0.839    532   0.753   3639   0.827  0.986  0.9192  0.9405  0.8398  0.9258
  0.1035   4054   0.780    530   0.692   4584   0.769  0.997  0.8675  0.9071  0.7814  0.9119
  0.1448   4877   0.646    540   0.597   5417   0.641  0.814  0.7750  0.8014  0.6890  0.8558
  0.1860   5601   0.382    531   0.335   6132   0.378  0.549  0.4930  0.4774  0.6938  0.7180
 $$
Resolution limits                    =     47.324     2.200
Number of used reflections           =      21886
Percentage observed                  =    99.7960
Percentage of free reflections       =     4.8269
Overall R factor                     =     0.2302
Free R factor                        =     0.3024
Average Fourier shell correlation    =     0.7693
AverageFree Fourier shell correlation=     0.7585
Overall weighted R factor            =     0.2118
Free weighted R factor               =     0.2852
Overall weighted R2 factor           =     0.2350
Free weighted R2 factor              =     0.3139
Average correlation coefficient      =     0.8466
Overall correlation coefficient      =     0.9550
Free correlation coefficient         =     0.9170
Cruickshanks DPI for coordinate error=     0.2182
DPI based on free R factor           =     0.2187
Overall figure of merit              =     0.6399
ML based su of positional parameters =     0.2552
ML based su of thermal parameters    =    11.3511
-----------------------------------------------------------------------------
 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    95892.688       17055.191       1934360.6      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   6.00000024E-02
 Actual weight    19.786564      is applied to the X-ray term


 function value    1905288.3    

-------------------------------------------------------------------------------
             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 =     1.4731, B  =   -0.1746
Partial structure    1: scale =     0.3712, B  =   52.2366
Overall anisotropic scale factors
   B11 =   5.72 B22 =  -1.88 B33 =  -3.85 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2295
Free R factor                        =     0.3016
Average Fourier shell correlation    =     0.7646
AverageFree Fourier shell correlation=     0.7547
Average correlation coefficient      =     0.8486
Overall figure of merit              =     0.6224
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    95725.641       11206.762       1905288.3       1934360.6    


     CGMAT cycle number =      3

 Weight matrix   5.99999987E-02
 Actual weight    19.686449      is applied to the X-ray term


 function value    1894980.4    

-------------------------------------------------------------------------------
             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 =     1.4734, B  =    0.0329
Partial structure    1: scale =     0.3710, B  =   52.1220
Overall anisotropic scale factors
   B11 =   5.70 B22 =  -1.85 B33 =  -3.85 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2289
Free R factor                        =     0.3023
Average Fourier shell correlation    =     0.7684
AverageFree Fourier shell correlation=     0.7574
Average correlation coefficient      =     0.8491
Overall figure of merit              =     0.6260
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    95675.273       11473.990       1894980.4       1905288.3    


     CGMAT cycle number =      4

 Weight matrix   5.99999949E-02
 Actual weight    19.545929      is applied to the X-ray term


 function value    1880634.5    

-------------------------------------------------------------------------------
             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 =     1.4754, B  =    0.0530
Partial structure    1: scale =     0.3709, B  =   52.1354
Overall anisotropic scale factors
   B11 =   5.67 B22 =  -1.84 B33 =  -3.84 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2287
Free R factor                        =     0.3024
Average Fourier shell correlation    =     0.7707
AverageFree Fourier shell correlation=     0.7593
Average correlation coefficient      =     0.8496
Overall figure of merit              =     0.6283
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    95628.438       11487.816       1880634.5       1894980.4    


     CGMAT cycle number =      5

 Weight matrix   5.99999987E-02
 Actual weight    19.457745      is applied to the X-ray term


 function value    1871824.4    

-------------------------------------------------------------------------------
             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 =     1.4758, B  =    0.0023
Partial structure    1: scale =     0.3708, B  =   52.2506
Overall anisotropic scale factors
   B11 =   5.65 B22 =  -1.82 B33 =  -3.84 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2285
Free R factor                        =     0.3026
Average Fourier shell correlation    =     0.7723
AverageFree Fourier shell correlation=     0.7605
Average correlation coefficient      =     0.8501
Overall figure of merit              =     0.6298
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03
 fvalues    95607.641       11515.345       1871824.4       1880634.5    


     CGMAT cycle number =      6

 Weight matrix   5.99999949E-02
 Actual weight    19.492655      is applied to the X-ray term


 function value    1875193.3    

-------------------------------------------------------------------------------
             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 =     1.4757, B  =   -0.0084
Partial structure    1: scale =     0.3706, B  =   52.2031
Overall anisotropic scale factors
   B11 =   5.65 B22 =  -1.81 B33 =  -3.83 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2283
Free R factor                        =     0.3024
Average Fourier shell correlation    =     0.7718
AverageFree Fourier shell correlation=     0.7601
Average correlation coefficient      =     0.8505
Overall figure of merit              =     0.6290
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    95608.477       11538.265       1874747.0       1871824.4    
 fvalues    95608.477       11538.265       1874747.0       1875201.3    


     CGMAT cycle number =      7

 Weight matrix   6.00000024E-02
 Actual weight    19.516165      is applied to the X-ray term


 function value    1877220.0    

-------------------------------------------------------------------------------
             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 =     1.4765, B  =    0.0006
Partial structure    1: scale =     0.3709, B  =   51.9515
Overall anisotropic scale factors
   B11 =   5.63 B22 =  -1.81 B33 =  -3.82 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2281
Free R factor                        =     0.3025
Average Fourier shell correlation    =     0.7720
AverageFree Fourier shell correlation=     0.7603
Average correlation coefficient      =     0.8504
Overall figure of merit              =     0.6290
-----------------------------------------------------------------------------
 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    95585.617       11583.523       1876841.6       1875201.3    
 fvalues    95585.617       11583.523       1876841.6       1877048.1    


     CGMAT cycle number =      8

 Weight matrix   5.99999987E-02
 Actual weight    19.531441      is applied to the X-ray term


 function value    1878508.3    

-------------------------------------------------------------------------------
             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 =     1.4771, B  =   -0.0008
Partial structure    1: scale =     0.3710, B  =   51.7608
Overall anisotropic scale factors
   B11 =   5.62 B22 =  -1.80 B33 =  -3.82 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2280
Free R factor                        =     0.3025
Average Fourier shell correlation    =     0.7722
AverageFree Fourier shell correlation=     0.7603
Average correlation coefficient      =     0.8504
Overall figure of merit              =     0.6290
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02


 fvalues    95583.109       11588.798       1878336.4       1877048.1    
 fvalues    95583.109       11588.798       1878336.4       1878464.6    


     CGMAT cycle number =      9

 Weight matrix   5.99999987E-02
 Actual weight    19.550688      is applied to the X-ray term


 function value    1880301.1    

-------------------------------------------------------------------------------
             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 =     1.4773, B  =   -0.0061
Partial structure    1: scale =     0.3710, B  =   51.7961
Overall anisotropic scale factors
   B11 =   5.61 B22 =  -1.79 B33 =  -3.82 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2279
Free R factor                        =     0.3025
Average Fourier shell correlation    =     0.7723
AverageFree Fourier shell correlation=     0.7604
Average correlation coefficient      =     0.8505
Overall figure of merit              =     0.6290
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02


 fvalues    95579.219       11616.738       1880691.6       1878464.6    

 fvalues    95579.219       11616.738       1880714.4       1880256.3    
 fvalues    95579.219       11616.738       1880714.4       1880256.3    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   100  140  160
 Maximuum H,K,L                 :    27   37   44
 Minimum acceptable grid spacing:    66   91  107
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   100  140  160
 Maximuum H,K,L                 :    27   37   44
 Minimum acceptable grid spacing:    66   91  107
 Weight matrix   5.99999987E-02
 Actual weight    19.802797      is applied to the X-ray term
Norm of X_ray positional gradient                30.8
Norm of Geom. positional gradient                30.4
Norm of X_ray B-factor gradient                  32.8
Norm of Geom. B-factor gradient                  32.1
Product of X_ray and Geom posit. gradients     -0.125E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.471E+07
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.1893E+07 GEOM=     0.1162E+05 TOTAL=     0.1905E+07
 function value    1904502.0    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   3054     1.926     1.648
Bond angles  : others                          5121     1.376     1.582
Torsion angles, period  1. refined              265     7.697     5.000
Torsion angles, period  2. refined              135    33.250    22.370
Torsion angles, period  3. refined              475    20.746    15.000
Torsion angles, period  4. refined               19    20.881    15.000
Chiral centres: refined atoms                   284     0.084     0.200
Planar groups: refined atoms                   2462     0.010     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   525     0.230     0.200
VDW repulsions.others                          2032     0.191     0.200
VDW; torsion: refined_atoms                    1096     0.172     0.200
VDW; torsion.others                            1116     0.089     0.200
HBOND: refined_atoms                             53     0.183     0.200
VDW repulsions: symmetry: refined_atoms           7     0.249     0.200
VDW repulsions: symmetry: others                 34     0.230     0.200
HBOND: symmetry: refined_atoms                    2     0.146     0.200
M. chain bond B values: refined atoms          1075     8.002     6.988
M. chain bond B values: others                 1074     8.002     6.979
M. chain angle B values: refined atoms         1335    10.429    10.422
M. chain angle B values: others                1336    10.430    10.431
S. chain bond B values: refined atoms          1209     9.381     7.891
S. chain bond B values: others                 1207     9.379     7.884
S. chain angle B values: refined atoms         1719    13.203    11.447
S. chain angle B values: others                1719    13.199    11.447
Long range B values: refined atoms             2606    15.415    79.731
Long range B values: others                    2606    15.423    79.770
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4785, B  =    0.0082
Partial structure    1: scale =     0.3712, B  =   51.8928
Overall anisotropic scale factors
   B11 =   5.60 B22 =  -1.78 B33 =  -3.81 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.021    2114  99.33   289.6   287.7  0.22  0.23     106   268.7   272.8  0.31  0.32
 0.062    3639  99.84   199.2   189.4  0.18  0.18     173   203.8   189.2  0.25  0.24
 0.104    4584  99.69    87.0    78.0  0.23  0.21     262    84.8    79.3  0.32  0.29
 0.145    5417  99.93    40.4    39.9  0.29  0.25     276    43.1    42.9  0.36  0.32
 0.186    6128  99.92    25.9    22.7  0.39  0.37     292    26.6    24.1  0.42  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0211   1602   0.825    512   0.760   2114   0.809  0.917  0.9221  0.9429  0.8715  0.9188
  0.0623   3107   0.842    532   0.756   3639   0.830  0.987  0.9209  0.9432  0.8411  0.9299
  0.1035   4054   0.779    530   0.692   4584   0.769  0.997  0.8642  0.9062  0.7758  0.9106
  0.1448   4877   0.655    540   0.604   5417   0.650  0.814  0.7844  0.8090  0.6927  0.8571
  0.1860   5601   0.312    531   0.283   6132   0.309  0.423  0.4793  0.4661  0.6895  0.7290
 $$
Resolution limits                    =     47.324     2.200
Number of used reflections           =      21886
Percentage observed                  =    99.7960
Percentage of free reflections       =     4.8269
Overall R factor                     =     0.2279
Free R factor                        =     0.3025
Average Fourier shell correlation    =     0.7685
AverageFree Fourier shell correlation=     0.7571
Overall weighted R factor            =     0.2096
Free weighted R factor               =     0.2852
Overall weighted R2 factor           =     0.2327
Free weighted R2 factor              =     0.3128
Average correlation coefficient      =     0.8505
Overall correlation coefficient      =     0.9558
Free correlation coefficient         =     0.9177
Cruickshanks DPI for coordinate error=     0.2160
DPI based on free R factor           =     0.2188
Overall figure of merit              =     0.6246
ML based su of positional parameters =     0.2537
ML based su of thermal parameters    =    11.3572
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    95557.133       11620.654       1904502.9       1880256.3    

 fvalues    95557.133       11620.654       1904494.4       1903919.1    
 fvalues    95557.133       11620.654       1904494.4       1903919.1    

 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_2-20A.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     1.927     1.648
Bond angles  : others                          5121     1.376     1.582
Torsion angles, period  1. refined              265     7.701     5.000
Torsion angles, period  2. refined              135    33.258    22.370
Torsion angles, period  3. refined              475    20.752    15.000
Torsion angles, period  4. refined               19    20.897    15.000
Chiral centres: refined atoms                   284     0.084     0.200
Planar groups: refined atoms                   2462     0.010     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   526     0.230     0.200
VDW repulsions.others                          2033     0.191     0.200
VDW; torsion: refined_atoms                    1096     0.172     0.200
VDW; torsion.others                            1118     0.089     0.200
HBOND: refined_atoms                             53     0.183     0.200
VDW repulsions: symmetry: refined_atoms           7     0.249     0.200
VDW repulsions: symmetry: others                 34     0.230     0.200
HBOND: symmetry: refined_atoms                    2     0.146     0.200
M. chain bond B values: refined atoms          1075     8.007     6.988
M. chain bond B values: others                 1074     8.007     6.979
M. chain angle B values: refined atoms         1335    10.434    10.422
M. chain angle B values: others                1336    10.435    10.431
S. chain bond B values: refined atoms          1209     9.387     7.892
S. chain bond B values: others                 1207     9.386     7.884
S. chain angle B values: refined atoms         1719    13.209    11.447
S. chain angle B values: others                1719    13.205    11.448
Long range B values: refined atoms             2607    15.416    79.745
Long range B values: others                    2607    15.423    79.784
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4788, B  =    0.0049
Partial structure    1: scale =     0.3712, B  =   51.8913
Overall anisotropic scale factors
   B11 =   5.59 B22 =  -1.78 B33 =  -3.81 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.021    2114  99.33   289.5   287.7  0.22  0.23     106   268.7   272.8  0.31  0.32
 0.062    3639  99.84   199.2   189.4  0.18  0.18     173   203.8   189.1  0.25  0.24
 0.104    4584  99.69    86.9    78.0  0.23  0.21     262    84.8    79.3  0.32  0.29
 0.145    5417  99.93    40.4    39.9  0.29  0.25     276    43.1    42.9  0.36  0.32
 0.186    6128  99.92    25.9    22.7  0.39  0.37     292    26.5    24.1  0.42  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0211   1602   0.825    512   0.760   2114   0.809  0.917  0.9220  0.9429  0.8712  0.9189
  0.0623   3107   0.843    532   0.757   3639   0.830  0.987  0.9211  0.9433  0.8413  0.9299
  0.1035   4054   0.779    530   0.692   4584   0.769  0.997  0.8642  0.9062  0.7754  0.9106
  0.1448   4877   0.655    540   0.605   5417   0.650  0.814  0.7845  0.8091  0.6923  0.8571
  0.1860   5601   0.310    531   0.281   6132   0.307  0.420  0.4775  0.4642  0.6894  0.7289
 $$
Resolution limits                    =     47.324     2.200
Number of used reflections           =      21886
Percentage observed                  =    99.7960
Percentage of free reflections       =     4.8269
Overall R factor                     =     0.2279
Free R factor                        =     0.3027
Average Fourier shell correlation    =     0.7680
AverageFree Fourier shell correlation=     0.7567
Overall weighted R factor            =     0.2096
Free weighted R factor               =     0.2853
Overall weighted R2 factor           =     0.2326
Free weighted R2 factor              =     0.3130
Average correlation coefficient      =     0.8505
Overall correlation coefficient      =     0.9558
Free correlation coefficient         =     0.9176
Cruickshanks DPI for coordinate error=     0.2160
DPI based on free R factor           =     0.2190
Overall figure of merit              =     0.6241
ML based su of positional parameters =     0.2537
ML based su of thermal parameters    =    11.3572
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.09
             Elapsed =         128.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2302   0.3024   0.640       95893.    5008.5   0.0117  0.819   1.829  1.089   0.081
       1   0.2295   0.3016   0.622       95726.    5007.2   0.0122  0.851   1.855  1.103   0.082
       2   0.2289   0.3023   0.626       95675.    5007.2   0.0124  0.862   1.889  1.122   0.083
       3   0.2287   0.3024   0.628       95628.    5005.5   0.0123  0.857   1.900  1.127   0.083
       4   0.2285   0.3026   0.630       95608.    5005.2   0.0123  0.855   1.907  1.130   0.083
       5   0.2283   0.3024   0.629       95608.    5005.7   0.0123  0.853   1.912  1.133   0.084
       6   0.2281   0.3025   0.629       95594.    5005.8   0.0123  0.855   1.920  1.136   0.084
       7   0.2280   0.3025   0.629       95585.    5005.4   0.0123  0.854   1.922  1.137   0.084
       8   0.2279   0.3025   0.629       95582.    5005.6   0.0123  0.854   1.925  1.139   0.084
       9   0.2279   0.3025   0.625       95587.    5005.4   0.0123  0.854   1.926  1.139   0.084
      10   0.2279   0.3027   0.624       95584.    5005.3   0.0123  0.855   1.927  1.139   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2302   0.2279
             R free    0.3024   0.3027
     Rms BondLength    0.0117   0.0123
      Rms BondAngle    1.8295   1.9268
     Rms ChirVolume    0.0809   0.0838
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      64.3s System:    0.2s Elapsed:     1:05  
</pre>
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