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 ### CCP4 8.0.007: Refmac          version 5.8.0403 : 11/30/22##
 ###############################################################
 User: unknown  Run date: 21/12/2022 Run time: 13:04:58 


 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.


 $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_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - poli_ccp4sw2023_R00_2-10A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_ccp4sw2023_R00_2-00A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli_ccp4sw2023_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 : /opt/ccp4/ccp4-8.0/lib/data/monomers/mon*cif
Parameters for neW entry and VDW: /opt/ccp4/ccp4-8.0/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 :poli_ccp4sw2023_R00_2-10A.pdb
  NUMBER OF MONOMERS IN THE LIBRARY          : 35279
                with complete description    : 35279
  NUMBER OF MODIFICATIONS                    :   119
  NUMBER OF LINKS                            :    98
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  set_mod
  Number of atoms    :    2286
  Number of residues :     307
  Number of chains   :       3
 ---------
  I am reading library. Please wait.
                mon_lib.cif


                ******Default connectivity*******


                    **** Automatic generation of links ****

   Link info given in this sectoion is for information only
   If you want to use this links then either add them into the pdb/mmcif file or use make link yes option

  In create description
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  A1_  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  A1_  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  B2_  is missing in the structure
  ATTENTION: atom:OXT  THR                70  B2_  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  B2_  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
  In create description
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  A1_  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  A1_  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  B2_  is missing in the structure
  ATTENTION: atom:OXT  THR                70  B2_  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  B2_  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           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :    4571
  Number of angles restraints   :    8304
  Number of torsions restraints :    2161
  Number of chiralities         :     329
  Number of planar groups       :     746

 Scattering factors file : /opt/ccp4/ccp4-8.0/lib/data/atomsf.lib


_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
  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
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  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:      4571         0      4571
               Angles:      8304         0      8304
              Chirals:       329         0       329
               Planes:       746         0       746
             Torsions:      2161         0      2161
            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 =    7.49954796    



######  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    5.99999949E-02
 Actual weight    25.0216007      is applied to the X-ray term
Norm of X_ray positional gradient                39.2
Norm of Geom. positional gradient                44.0
Norm of X_ray B-factor gradient                  38.1
Norm of Geom. B-factor gradient                  29.9
Product of X_ray and Geom posit. gradients     -0.175E+08
 Cosine of angle between them                      -0.742
Product of X_ray and Geom B-fact gradients     -0.404E+07
 Cosine of angle between them                      -0.776


Residuals: XRAY=     0.2987E+07 GEOM=     0.1264E+05 TOTAL=     0.3000E+07
 function value    2999565.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.002     0.016
Bond angles  : refined atoms                   3054     1.966     1.652
Bond angles  : others                          5250     0.963     1.577
Torsion angles, period  1. refined              265     7.442     5.000
Torsion angles, period  2. refined               19     9.058     5.000
Torsion angles, period  3. refined              475    20.717    10.000
Torsion angles, period  6. refined              116    15.588    10.000
Chiral centres: refined atoms                   329     0.083     0.200
Planar groups: refined atoms                   2643     0.010     0.020
Planar groups: others                           553     0.013     0.020
VDW repulsions: refined_atoms                   555     0.249     0.200
VDW repulsions.others                          2135     0.221     0.200
VDW; torsion: refined_atoms                    1118     0.193     0.200
VDW; torsion.others                            1353     0.089     0.200
HBOND: refined_atoms                             57     0.197     0.200
VDW repulsions: symmetry: refined_atoms           8     0.189     0.200
VDW repulsions: symmetry: others                 37     0.252     0.200
HBOND: symmetry: refined_atoms                    3     0.154     0.200
M. chain bond B values: refined atoms          1075     8.390     6.910
M. chain bond B values: others                 1075     8.347     6.907
M. chain angle B values: refined atoms         1335    10.581    12.357
M. chain angle B values: others                1336    10.581    12.365
S. chain bond B values: refined atoms          1209     9.963     7.730
S. chain bond B values: others                 1210     9.959     7.733
S. chain angle B values: refined atoms         1719    13.856    13.837
S. chain angle B values: others                1720    13.852    13.839
Long range B values: refined atoms             2666    15.442    65.986
Long range B values: others                    2666    15.450    66.003
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4837, B  =   -1.1545
Partial structure    1: scale =     0.3909, B  =   56.8442
Overall anisotropic scale factors
   B11 =   4.98 B22 =  -1.53 B33 =  -3.45 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.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   278.0   276.0  0.20  0.21     125   267.0   267.3  0.30  0.31
 0.075    4806  99.90   159.3   146.5  0.20  0.19     260   161.4   148.4  0.27  0.25
 0.125    6062  99.74    55.6    54.7  0.25  0.21     344    55.4    55.8  0.34  0.31
 0.175    7199  99.91    28.8    27.3  0.36  0.33     331    29.4    28.2  0.39  0.36
 0.225    8050  99.26    20.4    13.3  0.48  0.48     417    20.1    12.9  0.47  0.47
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.815    625   0.748   2782   0.799  0.922  0.9386  0.9728  0.8473  0.9295
  0.0753   4157   0.823    649   0.743   4806   0.813  1.010  0.9520  0.9764  0.8495  0.9332
  0.1252   5428   0.708    634   0.641   6062   0.701  0.874  0.9250  0.9598  0.7292  0.8881
  0.1751   6547   0.500    652   0.455   7199   0.496  0.651  0.8573  0.8794  0.7055  0.7758
  0.2250   7412   0.220    645   0.199   8057   0.218  0.376  0.7254  0.6909  0.5887  0.5573
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2419
Free R factor                        =     0.3162
Average Fourier shell correlation    =     0.8688
AverageFree Fourier shell correlation=     0.8594
Overall weighted R factor            =     0.2147
Free weighted R factor               =     0.2913
Overall weighted R2 factor           =     0.2283
Free weighted R2 factor              =     0.3177
Average correlation coefficient      =     0.7795
Overall correlation coefficient      =     0.9615
Free correlation coefficient         =     0.9185
Cruickshanks DPI for coordinate error=     0.1675
DPI based on free R factor           =     0.1810
Overall figure of merit              =     0.5432
ML based su of positional parameters =     0.2707
ML based su of thermal parameters    =    11.7159
-----------------------------------------------------------------------------
 iters          800   9.27756361E-08   1.83787030E-09  0.461798519       3.97980982E-09
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    5.24999984E-02   0.00000000    
 Gamma decreased to    4.19999994E-02
  Iterations           67
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.63820951E-04  0.121403076       1.09347608E-02
   2999565.25       0.00000000       1.00000000       1.00000000     T
 fvalues    119374.047       12635.5918       2999565.25       1.00000003E+32


     CGMAT cycle number =        2

 Weight matrix    6.00000024E-02
 Actual weight    24.0079098      is applied to the X-ray term


 function value    2871257.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4887, B  =   -0.1501
Partial structure    1: scale =     0.3925, B  =   56.2995
Overall anisotropic scale factors
   B11 =   4.90 B22 =  -1.51 B33 =  -3.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3157
Average Fourier shell correlation    =     0.8690
AverageFree Fourier shell correlation=     0.8595
Average correlation coefficient      =     0.7816
Overall figure of merit              =     0.5401
-----------------------------------------------------------------------------
 Gamma decreased to    3.24545428E-02
  Iterations           78
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.01374731E-04  0.188058972       8.44624545E-03
   2871257.50       2999565.25       1.00000000       1.00000000     F
 fvalues    119093.086       12081.4531       2871257.50       2999565.25    


     CGMAT cycle number =        3

 Weight matrix    6.00000024E-02
 Actual weight    23.5139561      is applied to the X-ray term


 function value    2810190.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4902, B  =    0.1266
Partial structure    1: scale =     0.3932, B  =   56.1708
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.50 B33 =  -3.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3170
Average Fourier shell correlation    =     0.8711
AverageFree Fourier shell correlation=     0.8608
Average correlation coefficient      =     0.7805
Overall figure of merit              =     0.5461
-----------------------------------------------------------------------------
 Gamma decreased to    2.37768572E-02
  Iterations           90
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.44479302E-04  0.210376054       9.02331155E-03
   2810190.25       2871257.50       1.00000000       1.00000000     F
 fvalues    118987.523       12322.7080       2810190.25       2871257.50    


     CGMAT cycle number =        4

 Weight matrix    6.00000024E-02
 Actual weight    24.1081047      is applied to the X-ray term


 function value    2882051.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4911, B  =    0.0662
Partial structure    1: scale =     0.3934, B  =   56.1164
Overall anisotropic scale factors
   B11 =   4.85 B22 =  -1.49 B33 =  -3.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3166
Average Fourier shell correlation    =     0.8698
AverageFree Fourier shell correlation=     0.8597
Average correlation coefficient      =     0.7811
Overall figure of merit              =     0.5394
-----------------------------------------------------------------------------
 Gamma decreased to    1.58880539E-02
  Iterations          105
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts    1.18316684E-05  0.139428958       6.34320406E-03
   2882051.50       2810190.25      0.618034005      0.618034005     T
 fvalues    119039.492       12235.0117       2882051.50       2810190.25    


     CGMAT cycle number =        5

 Weight matrix    6.00000024E-02
 Actual weight    24.4367390      is applied to the X-ray term


 function value    2922232.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4912, B  =    0.0488
Partial structure    1: scale =     0.3936, B  =   56.2736
Overall anisotropic scale factors
   B11 =   4.82 B22 =  -1.48 B33 =  -3.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3172
Average Fourier shell correlation    =     0.8688
AverageFree Fourier shell correlation=     0.8588
Average correlation coefficient      =     0.7806
Overall figure of merit              =     0.5365
-----------------------------------------------------------------------------
 Gamma decreased to    8.71641375E-03
  Iterations          129
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -2.73372025E-05   8.31578821E-02   4.92477510E-03
   2922232.00       2882051.50      0.381966025      0.381966025     T
 fvalues    119078.242       12348.0000       2922232.00       2882051.50    


     CGMAT cycle number =        6

 Weight matrix    5.99999949E-02
 Actual weight    23.2516689      is applied to the X-ray term


 function value    2777628.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4922, B  =    0.0737
Partial structure    1: scale =     0.3942, B  =   56.4205
Overall anisotropic scale factors
   B11 =   4.81 B22 =  -1.48 B33 =  -3.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2412
Free R factor                        =     0.3176
Average Fourier shell correlation    =     0.8723
AverageFree Fourier shell correlation=     0.8616
Average correlation coefficient      =     0.7803
Overall figure of merit              =     0.5491
-----------------------------------------------------------------------------
 Gamma decreased to    2.19674082E-03
  Iterations          171
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -7.71389241E-05  0.114512838       6.85103051E-03
   2777628.50       2922232.00      0.381966025      0.381966025     F
 fvalues    118925.781       12405.3750       2777628.50       2922232.00    


     CGMAT cycle number =        7

 Weight matrix    5.99999987E-02
 Actual weight    23.9641552      is applied to the X-ray term


 function value    2863980.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4928, B  =    0.0518
Partial structure    1: scale =     0.3943, B  =   56.4283
Overall anisotropic scale factors
   B11 =   4.80 B22 =  -1.47 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2414
Free R factor                        =     0.3175
Average Fourier shell correlation    =     0.8708
AverageFree Fourier shell correlation=     0.8602
Average correlation coefficient      =     0.7806
Overall figure of merit              =     0.5416
-----------------------------------------------------------------------------
 Gamma decreased to    0.00000000    
  Iterations          347
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.06769312E-05  0.143297896       8.32832977E-03
   2863980.00       2777628.50      0.236067981      0.236067981     T
 fvalues    118996.836       12321.3008       2863980.00       2777628.50    


     CGMAT cycle number =        8

 Weight matrix    6.00000024E-02
 Actual weight    24.3446445      is applied to the X-ray term


 function value    2909860.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4936, B  =    0.0510
Partial structure    1: scale =     0.3943, B  =   56.3196
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.47 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3176
Average Fourier shell correlation    =     0.8695
AverageFree Fourier shell correlation=     0.8591
Average correlation coefficient      =     0.7805
Overall figure of merit              =     0.5376
-----------------------------------------------------------------------------
 iters          800   3.81663092E-08   1.70491399E-09  0.370971411       4.59580951E-09
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    2.82878354E-02   0.00000000    
 Gamma decreased to    2.26302687E-02
  Iterations           95
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts    7.28695250E-06   2.74815448E-02   1.54300919E-03
   2909860.25       2863980.00      0.200000003      0.200000003     T
 fvalues    119021.211       12331.3535       2909860.25       2863980.00    


     CGMAT cycle number =        9

 Weight matrix    5.99999987E-02
 Actual weight    23.4856014      is applied to the X-ray term


 function value    2804873.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4946, B  =    0.0750
Partial structure    1: scale =     0.3945, B  =   56.3596
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.47 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3176
Average Fourier shell correlation    =     0.8719
AverageFree Fourier shell correlation=     0.8610
Average correlation coefficient      =     0.7804
Overall figure of merit              =     0.5465
-----------------------------------------------------------------------------
 Gamma decreased to    1.74870268E-02
  Iterations          107
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.11869504E-05   3.08198519E-02   1.75019761E-03
   2804873.75       2909860.25      0.200000003      0.200000003     F
 fvalues    118903.227       12360.0000       2804873.75       2909860.25    


     CGMAT cycle number =       10

 Weight matrix    5.99999949E-02
 Actual weight    24.0473099      is applied to the X-ray term


 function value    2873240.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4948, B  =    0.0358
Partial structure    1: scale =     0.3945, B  =   56.4017
Overall anisotropic scale factors
   B11 =   4.79 B22 =  -1.47 B33 =  -3.32 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3178
Average Fourier shell correlation    =     0.8703
AverageFree Fourier shell correlation=     0.8599
Average correlation coefficient      =     0.7805
Overall figure of merit              =     0.5405
-----------------------------------------------------------------------------
 Gamma decreased to    1.28113516E-02
  Iterations          122
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.31348628E-07   3.73102166E-02   2.08879635E-03
   2873240.50       2804873.75      0.200000003      0.200000003     T
 fvalues    118969.609       12341.4863       2873240.50       2804873.75    

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: poli_ccp4sw2023_R00_2-00A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
Bond angles  : refined atoms                   3054     2.064     1.652
Bond angles  : others                          5250     0.635     1.577
Torsion angles, period  1. refined              265     7.618     5.000
Torsion angles, period  2. refined               19    10.492     5.000
Torsion angles, period  3. refined              475    20.820    10.000
Torsion angles, period  6. refined              116    15.738    10.000
Chiral centres: refined atoms                   329     0.086     0.200
Planar groups: refined atoms                   2643     0.011     0.020
Planar groups: others                           553     0.001     0.020
VDW repulsions: refined_atoms                   569     0.254     0.200
VDW repulsions.others                          2163     0.205     0.200
VDW; torsion: refined_atoms                    1135     0.194     0.200
VDW; torsion.others                            1326     0.090     0.200
HBOND: refined_atoms                             59     0.203     0.200
HBOND.others                                      1     0.023     0.200
VDW repulsions: symmetry: refined_atoms           7     0.202     0.200
VDW repulsions: symmetry: others                 37     0.215     0.200
HBOND: symmetry: refined_atoms                    3     0.137     0.200
M. chain bond B values: refined atoms          1075     8.780     6.818
M. chain bond B values: others                 1075     8.763     6.816
M. chain angle B values: refined atoms         1335    11.010    12.184
M. chain angle B values: others                1336    11.010    12.192
S. chain bond B values: refined atoms          1209    10.399     7.676
S. chain bond B values: others                 1210    10.395     7.679
S. chain angle B values: refined atoms         1719    14.390    13.707
S. chain angle B values: others                1720    14.386    13.710
Long range B values: refined atoms             2689    16.048    65.128
Long range B values: others                    2688    16.055    65.144
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4940, B  =    0.0091
Partial structure    1: scale =     0.3945, B  =   56.4511
Overall anisotropic scale factors
   B11 =   4.78 B22 =  -1.47 B33 =  -3.32 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.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   276.1   275.1  0.20  0.21     125   265.2   266.0  0.30  0.31
 0.075    4806  99.90   158.2   145.5  0.20  0.18     260   160.3   147.1  0.27  0.26
 0.125    6062  99.74    55.2    54.5  0.25  0.22     344    55.0    55.8  0.35  0.32
 0.175    7199  99.91    28.6    27.3  0.35  0.33     331    29.2    28.2  0.38  0.35
 0.225    8050  99.26    20.2    13.3  0.47  0.47     417    20.0    12.8  0.46  0.47
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.826    625   0.758   2782   0.811  0.921  0.9394  0.9730  0.8460  0.9299
  0.0753   4157   0.822    649   0.743   4806   0.811  1.010  0.9519  0.9771  0.8508  0.9353
  0.1252   5428   0.726    634   0.658   6062   0.719  0.878  0.9236  0.9594  0.7188  0.8859
  0.1751   6547   0.458    652   0.420   7199   0.455  0.601  0.8484  0.8705  0.7035  0.7815
  0.2250   7412   0.217    645   0.196   8057   0.215  0.372  0.7318  0.7001  0.5862  0.5558
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2413
Free R factor                        =     0.3178
Average Fourier shell correlation    =     0.8692
AverageFree Fourier shell correlation=     0.8589
Overall weighted R factor            =     0.2141
Free weighted R factor               =     0.2933
Overall weighted R2 factor           =     0.2279
Free weighted R2 factor              =     0.3198
Average correlation coefficient      =     0.7804
Overall correlation coefficient      =     0.9619
Free correlation coefficient         =     0.9179
Cruickshanks DPI for coordinate error=     0.1671
DPI based on free R factor           =     0.1819
Overall figure of merit              =     0.5370
ML based su of positional parameters =     0.2654
ML based su of thermal parameters    =    11.5470
-----------------------------------------------------------------------------
  Time in seconds: CPU =        10.35
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2419   0.3162   0.543      119374.    6243.7   0.0104  0.843   1.966  1.151   0.083
       1   0.2413   0.3157   0.540      119093.    6237.2   0.0112  0.901   2.006  1.174   0.084
       2   0.2413   0.3170   0.546      118988.    6234.6   0.0112  0.903   2.037  1.192   0.085
       3   0.2413   0.3166   0.539      119039.    6236.7   0.0111  0.893   2.038  1.191   0.085
       4   0.2412   0.3172   0.537      119078.    6239.2   0.0112  0.902   2.053  1.200   0.086
       5   0.2412   0.3176   0.549      118926.    6233.7   0.0112  0.906   2.062  1.205   0.086
       6   0.2414   0.3175   0.542      118997.    6236.3   0.0111  0.898   2.056  1.201   0.085
       7   0.2413   0.3176   0.538      119021.    6237.2   0.0111  0.899   2.059  1.203   0.086
       8   0.2413   0.3176   0.546      118903.    6232.4   0.0112  0.901   2.063  1.205   0.086
       9   0.2413   0.3178   0.540      118970.    6235.2   0.0111  0.899   2.062  1.204   0.086
      10   0.2413   0.3178   0.537      119023.    6237.6   0.0112  0.900   2.064  1.206   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2419   0.2413
             R free    0.3162   0.3178
     Rms BondLength    0.0104   0.0112
      Rms BondAngle    1.9659   2.0642
     Rms ChirVolume    0.0828   0.0856
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0403   
Times: User:      14.6s System:    0.1s Elapsed:     0:15