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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 28/ 5/2020 Run time: 11:02:49 


 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 2.00     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_2-10A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli67_R00_2-00A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli67_R00_2-00A.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       0.0500
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.0000
  Estimated number of reflections :      40320
  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  2.0000

  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_2-10A.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       1483
Number of   all  reflections      30492
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          30492

   Current auto weighting coefficient =    7.4995480    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Weight matrix   5.99999987E-02
 Actual weight    22.652088      is applied to the X-ray term
Norm of X_ray positional gradient                35.6
Norm of Geom. positional gradient                77.4
Norm of X_ray B-factor gradient                  38.3
Norm of Geom. B-factor gradient                  31.3
Product of X_ray and Geom posit. gradients     -0.133E+08
 Cosine of angle between them                      -0.359
Product of X_ray and Geom B-fact gradients     -0.439E+07
 Cosine of angle between them                      -0.816


Residuals: XRAY=     0.2692E+07 GEOM=     0.1856E+05 TOTAL=     0.2710E+07
 function value    2710188.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.971     1.648
Bond angles  : others                          5121     2.285     1.582
Torsion angles, period  1. refined              265     7.793     5.000
Torsion angles, period  2. refined              135    33.255    22.370
Torsion angles, period  3. refined              475    21.161    15.000
Torsion angles, period  4. refined               19    20.910    15.000
Chiral centres: refined atoms                   284     0.087     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.014     0.020
VDW repulsions: refined_atoms                   551     0.237     0.200
VDW repulsions.others                          1999     0.231     0.200
VDW; torsion: refined_atoms                    1094     0.176     0.200
VDW; torsion.others                            1064     0.083     0.200
HBOND: refined_atoms                             56     0.201     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms          11     0.220     0.200
VDW repulsions: symmetry: others                 34     0.243     0.200
HBOND: symmetry: refined_atoms                    2     0.138     0.200
M. chain bond B values: refined atoms          1075     7.845     6.962
M. chain bond B values: others                 1074     7.831     6.954
M. chain angle B values: refined atoms         1335     9.941    10.393
M. chain angle B values: others                1336     9.939    10.401
S. chain bond B values: refined atoms          1209     9.276     7.771
S. chain bond B values: others                 1207     9.279     7.764
S. chain angle B values: refined atoms         1719    12.748    11.312
S. chain angle B values: others                1719    12.745    11.312
Long range B values: refined atoms             2627    14.704    80.206
Long range B values: others                    2626    14.717    80.224
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5124, B  =   -1.2205
Partial structure    1: scale =     0.3866, B  =   55.5386
Overall anisotropic scale factors
   B11 =   5.00 B22 =  -1.53 B33 =  -3.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   272.7   271.0  0.20  0.21     125   261.9   260.5  0.30  0.30
 0.075    4806  99.90   156.3   144.4  0.20  0.18     260   158.4   146.5  0.27  0.25
 0.125    6062  99.74    54.5    53.7  0.25  0.21     344    54.4    55.2  0.35  0.32
 0.175    7199  99.91    28.2    26.7  0.36  0.33     331    28.8    27.7  0.39  0.36
 0.225    8050  99.26    20.0    12.8  0.48  0.48     417    19.7    12.3  0.48  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.814    625   0.748   2782   0.799  0.922  0.9096  0.9435  0.8536  0.9293
  0.0753   4157   0.824    649   0.742   4806   0.813  1.006  0.9136  0.9367  0.8511  0.9335
  0.1252   5428   0.704    634   0.638   6062   0.697  0.872  0.8295  0.8692  0.7270  0.8879
  0.1751   6547   0.498    652   0.452   7199   0.494  0.654  0.6251  0.6416  0.7054  0.7758
  0.2250   7412   0.274    645   0.249   8057   0.272  0.476  0.3008  0.2949  0.5853  0.5583
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2418
Free R factor                        =     0.3166
Average Fourier shell correlation    =     0.6708
AverageFree Fourier shell correlation=     0.6560
Overall weighted R factor            =     0.2140
Free weighted R factor               =     0.2903
Overall weighted R2 factor           =     0.2274
Free weighted R2 factor              =     0.3156
Average correlation coefficient      =     0.7797
Overall correlation coefficient      =     0.9616
Free correlation coefficient         =     0.9205
Cruickshanks DPI for coordinate error=     0.1674
DPI based on free R factor           =     0.1813
Overall figure of merit              =     0.5569
ML based su of positional parameters =     0.2716
ML based su of thermal parameters    =    11.8405
-----------------------------------------------------------------------------
 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    118824.88       18556.436       2710188.3      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   6.00000024E-02
 Actual weight    21.324308      is applied to the X-ray term


 function value    2541886.3    

-------------------------------------------------------------------------------
             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 =     1.5122, B  =   -0.1435
Partial structure    1: scale =     0.3864, B  =   55.3192
Overall anisotropic scale factors
   B11 =   4.93 B22 =  -1.51 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2411
Free R factor                        =     0.3152
Average Fourier shell correlation    =     0.6733
AverageFree Fourier shell correlation=     0.6595
Average correlation coefficient      =     0.7825
Overall figure of merit              =     0.5590
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    118608.37       12644.738       2541886.3       2710188.3    


     CGMAT cycle number =      3

 Weight matrix   6.00000024E-02
 Actual weight    20.470459      is applied to the X-ray term


 function value    2438354.3    

-------------------------------------------------------------------------------
             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
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5132, B  =    0.1329
Partial structure    1: scale =     0.3865, B  =   54.9436
Overall anisotropic scale factors
   B11 =   4.90 B22 =  -1.49 B33 =  -3.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3156
Average Fourier shell correlation    =     0.6820
AverageFree Fourier shell correlation=     0.6682
Average correlation coefficient      =     0.7818
Overall figure of merit              =     0.5707
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    118495.34       12700.345       2438354.3       2541886.3    


     CGMAT cycle number =      4

 Weight matrix   5.99999949E-02
 Actual weight    20.655849      is applied to the X-ray term


 function value    2460716.5    

-------------------------------------------------------------------------------
             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 =     1.5154, B  =    0.1496
Partial structure    1: scale =     0.3868, B  =   55.0129
Overall anisotropic scale factors
   B11 =   4.88 B22 =  -1.49 B33 =  -3.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3149
Average Fourier shell correlation    =     0.6826
AverageFree Fourier shell correlation=     0.6696
Average correlation coefficient      =     0.7827
Overall figure of merit              =     0.5683
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02


 fvalues    118444.58       12471.193       2460566.8       2438354.3    

 fvalues    118444.58       12471.193       2460428.3       2459044.5    
 fvalues    118444.58       12471.193       2460428.3       2459044.5    


     CGMAT cycle number =      5

 Weight matrix   5.99999949E-02
 Actual weight    20.675745      is applied to the X-ray term


 function value    2462767.8    

-------------------------------------------------------------------------------
             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 =     1.5162, B  =    0.1392
Partial structure    1: scale =     0.3868, B  =   55.0194
Overall anisotropic scale factors
   B11 =   4.88 B22 =  -1.48 B33 =  -3.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3150
Average Fourier shell correlation    =     0.6820
AverageFree Fourier shell correlation=     0.6689
Average correlation coefficient      =     0.7826
Overall figure of merit              =     0.5676
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    118431.75       12482.867       2462531.3       2459044.5    

 fvalues    118431.75       12482.867       2462627.3       2461147.5    
 fvalues    118431.75       12482.867       2462627.3       2461147.5    


     CGMAT cycle number =      6

 Weight matrix   5.99999987E-02
 Actual weight    20.701057      is applied to the X-ray term


 function value    2465620.0    

-------------------------------------------------------------------------------
             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 =     1.5165, B  =    0.1415
Partial structure    1: scale =     0.3868, B  =   54.9353
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.48 B33 =  -3.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3151
Average Fourier shell correlation    =     0.6817
AverageFree Fourier shell correlation=     0.6686
Average correlation coefficient      =     0.7825
Overall figure of merit              =     0.5672
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    118425.95       12485.642       2465529.3       2461147.5    

 fvalues    118425.95       12485.642       2465532.3       2464028.0    
 fvalues    118425.95       12485.642       2465532.3       2464028.0    


     CGMAT cycle number =      7

 Weight matrix   5.99999949E-02
 Actual weight    20.743668      is applied to the X-ray term


 function value    2470760.3    

-------------------------------------------------------------------------------
             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
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5164, B  =    0.1492
Partial structure    1: scale =     0.3868, B  =   54.9155
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.48 B33 =  -3.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3151
Average Fourier shell correlation    =     0.6815
AverageFree Fourier shell correlation=     0.6684
Average correlation coefficient      =     0.7825
Overall figure of merit              =     0.5669
-----------------------------------------------------------------------------
 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    118430.56       12486.641       2470659.5       2464028.0    

 fvalues    118430.56       12486.641       2470683.8       2469171.0    
 fvalues    118430.56       12486.641       2470683.8       2469171.0    


     CGMAT cycle number =      8

 Weight matrix   5.99999949E-02
 Actual weight    20.677475      is applied to the X-ray term


 function value    2462871.0    

-------------------------------------------------------------------------------
             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 =     1.5163, B  =    0.1061
Partial structure    1: scale =     0.3868, B  =   54.9257
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.48 B33 =  -3.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3151
Average Fourier shell correlation    =     0.6818
AverageFree Fourier shell correlation=     0.6687
Average correlation coefficient      =     0.7825
Overall figure of merit              =     0.5673
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02
 fvalues    118504.97       12487.383       2462871.0       2469171.0    


     CGMAT cycle number =      9

 Weight matrix   6.00000024E-02
 Actual weight    20.182436      is applied to the X-ray term


 function value    2402730.3    

-------------------------------------------------------------------------------
             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
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5163, B  =    0.1376
Partial structure    1: scale =     0.3867, B  =   54.9356
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.48 B33 =  -3.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3151
Average Fourier shell correlation    =     0.6859
AverageFree Fourier shell correlation=     0.6725
Average correlation coefficient      =     0.7825
Overall figure of merit              =     0.5743
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02
 fvalues    118431.77       12488.449       2402730.3       2462871.0    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Weight matrix   5.99999987E-02
 Actual weight    20.733061      is applied to the X-ray term
Norm of X_ray positional gradient                33.9
Norm of Geom. positional gradient                33.4
Norm of X_ray B-factor gradient                  36.1
Norm of Geom. B-factor gradient                  34.5
Product of X_ray and Geom posit. gradients     -0.152E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.552E+07
 Cosine of angle between them                      -0.989


Residuals: XRAY=     0.2457E+07 GEOM=     0.1249E+05 TOTAL=     0.2470E+07
 function value    2469502.0    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   3054     2.004     1.648
Bond angles  : others                          5121     1.408     1.582
Torsion angles, period  1. refined              265     7.847     5.000
Torsion angles, period  2. refined              135    33.024    22.370
Torsion angles, period  3. refined              475    21.245    15.000
Torsion angles, period  4. refined               19    20.381    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   554     0.240     0.200
VDW repulsions.others                          2023     0.208     0.200
VDW; torsion: refined_atoms                    1100     0.176     0.200
VDW; torsion.others                            1080     0.094     0.200
HBOND: refined_atoms                             59     0.204     0.200
VDW repulsions: symmetry: refined_atoms          10     0.235     0.200
VDW repulsions: symmetry: others                 36     0.226     0.200
HBOND: symmetry: refined_atoms                    2     0.124     0.200
M. chain bond B values: refined atoms          1075     7.956     6.846
M. chain bond B values: others                 1074     7.948     6.838
M. chain angle B values: refined atoms         1335    10.124    10.214
M. chain angle B values: others                1336    10.124    10.222
S. chain bond B values: refined atoms          1209     9.378     7.680
S. chain bond B values: others                 1207     9.380     7.673
S. chain angle B values: refined atoms         1719    12.928    11.164
S. chain angle B values: others                1719    12.923    11.164
Long range B values: refined atoms             2634    14.904    78.799
Long range B values: others                    2633    14.913    78.820
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5162, B  =    0.1243
Partial structure    1: scale =     0.3867, B  =   54.9239
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.48 B33 =  -3.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   272.0   271.0  0.20  0.21     125   261.3   260.3  0.30  0.30
 0.075    4806  99.90   155.9   144.1  0.19  0.18     260   158.0   146.1  0.26  0.25
 0.125    6062  99.74    54.4    53.7  0.26  0.22     344    54.2    55.3  0.35  0.32
 0.175    7199  99.91    28.1    26.7  0.36  0.33     331    28.7    27.8  0.39  0.36
 0.225    8050  99.26    19.9    12.8  0.48  0.48     417    19.7    12.3  0.47  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.827    625   0.759   2782   0.812  0.922  0.9118  0.9458  0.8529  0.9291
  0.0753   4157   0.824    649   0.742   4806   0.813  1.006  0.9146  0.9377  0.8538  0.9353
  0.1252   5428   0.727    634   0.657   6062   0.720  0.877  0.8389  0.8776  0.7230  0.8841
  0.1751   6547   0.470    652   0.429   7199   0.466  0.617  0.6139  0.6314  0.7091  0.7807
  0.2250   7412   0.313    645   0.286   8057   0.311  0.539  0.3447  0.3349  0.5911  0.5656
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2412
Free R factor                        =     0.3151
Average Fourier shell correlation    =     0.6816
AverageFree Fourier shell correlation=     0.6684
Overall weighted R factor            =     0.2134
Free weighted R factor               =     0.2892
Overall weighted R2 factor           =     0.2269
Free weighted R2 factor              =     0.3149
Average correlation coefficient      =     0.7825
Overall correlation coefficient      =     0.9617
Free correlation coefficient         =     0.9207
Cruickshanks DPI for coordinate error=     0.1670
DPI based on free R factor           =     0.1804
Overall figure of merit              =     0.5669
ML based su of positional parameters =     0.2596
ML based su of thermal parameters    =    11.2650
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    118549.79       12485.414       2468094.5       2402730.3    
 fvalues    118549.79       12485.414       2468094.5       2470385.5    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: poli67_R00_2-00A.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     2.005     1.648
Bond angles  : others                          5121     1.408     1.582
Torsion angles, period  1. refined              265     7.847     5.000
Torsion angles, period  2. refined              135    33.023    22.370
Torsion angles, period  3. refined              475    21.247    15.000
Torsion angles, period  4. refined               19    20.375    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   554     0.240     0.200
VDW repulsions.others                          2024     0.208     0.200
VDW; torsion: refined_atoms                    1100     0.176     0.200
VDW; torsion.others                            1080     0.094     0.200
HBOND: refined_atoms                             59     0.204     0.200
VDW repulsions: symmetry: refined_atoms          10     0.235     0.200
VDW repulsions: symmetry: others                 36     0.226     0.200
HBOND: symmetry: refined_atoms                    2     0.124     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    10.125    10.222
S. chain bond B values: refined atoms          1209     9.379     7.680
S. chain bond B values: others                 1207     9.381     7.674
S. chain angle B values: refined atoms         1719    12.929    11.164
S. chain angle B values: others                1719    12.924    11.165
Long range B values: refined atoms             2634    14.905    78.801
Long range B values: others                    2633    14.914    78.822
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5163, B  =    0.1001
Partial structure    1: scale =     0.3867, B  =   54.9386
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.48 B33 =  -3.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   272.0   271.0  0.20  0.21     125   261.3   260.3  0.30  0.30
 0.075    4806  99.90   155.9   144.2  0.19  0.18     260   158.0   146.1  0.26  0.25
 0.125    6062  99.74    54.4    53.7  0.26  0.22     344    54.2    55.3  0.35  0.32
 0.175    7199  99.91    28.1    26.7  0.36  0.33     331    28.7    27.8  0.39  0.36
 0.225    8050  99.26    19.9    12.8  0.47  0.48     417    19.7    12.3  0.47  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.827    625   0.759   2782   0.812  0.922  0.9119  0.9458  0.8531  0.9291
  0.0753   4157   0.824    649   0.742   4806   0.813  1.006  0.9146  0.9378  0.8537  0.9353
  0.1252   5428   0.727    634   0.657   6062   0.720  0.877  0.8390  0.8776  0.7232  0.8841
  0.1751   6547   0.495    652   0.452   7199   0.491  0.641  0.6292  0.6462  0.7088  0.7806
  0.2250   7412   0.313    645   0.286   8057   0.311  0.539  0.3448  0.3349  0.5909  0.5655
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2412
Free R factor                        =     0.3152
Average Fourier shell correlation    =     0.6853
AverageFree Fourier shell correlation=     0.6719
Overall weighted R factor            =     0.2134
Free weighted R factor               =     0.2892
Overall weighted R2 factor           =     0.2270
Free weighted R2 factor              =     0.3149
Average correlation coefficient      =     0.7824
Overall correlation coefficient      =     0.9617
Free correlation coefficient         =     0.9208
Cruickshanks DPI for coordinate error=     0.1670
DPI based on free R factor           =     0.1805
Overall figure of merit              =     0.5732
ML based su of positional parameters =     0.2596
ML based su of thermal parameters    =    11.2650
-----------------------------------------------------------------------------
  Time in seconds: CPU =        42.41
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2418   0.3166   0.557      118825.    6216.2   0.0126  0.873   1.971  1.165   0.087
       1   0.2411   0.3152   0.559      118608.    6213.1   0.0133  0.929   1.997  1.181   0.089
       2   0.2412   0.3156   0.571      118495.    6210.1   0.0133  0.921   2.013  1.191   0.089
       3   0.2412   0.3149   0.568      118526.    6209.5   0.0130  0.900   2.002  1.184   0.088
       4   0.2412   0.3150   0.568      118510.    6209.1   0.0130  0.902   2.003  1.185   0.088
       5   0.2412   0.3151   0.567      118503.    6208.9   0.0130  0.903   2.004  1.186   0.088
       6   0.2412   0.3151   0.567      118507.    6209.0   0.0130  0.903   2.004  1.186   0.088
       7   0.2412   0.3151   0.567      118505.    6209.2   0.0130  0.903   2.004  1.186   0.088
       8   0.2412   0.3151   0.574      118432.    6206.1   0.0130  0.903   2.005  1.186   0.088
       9   0.2412   0.3151   0.567      118507.    6209.2   0.0130  0.903   2.004  1.186   0.088
      10   0.2412   0.3152   0.573      118437.    6206.6   0.0130  0.903   2.005  1.186   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2418   0.2412
             R free    0.3166   0.3152
     Rms BondLength    0.0126   0.0130
      Rms BondAngle    1.9714   2.0045
     Rms ChirVolume    0.0869   0.0881
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      79.7s System:    0.2s Elapsed:     1:20  
</pre>
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