# Date 2007-12-01 Time 00:57:09 PST -0800 (1196499429.86 s)
#phil __OFF__

Command line arguments: "pdb1yfs_refine_002.def" "ordered_solvent=True"

HOST = rosie.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14318

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.ordered_solvent = True

Working crystal symmetry after inspecting all inputs:
  Unit cell: (173.026, 73.868, 73.999, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 7294
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 7294
      Number of chains: 3
        Number of residues, atoms: 448, 3641
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 19, 'TRANS': 428}
          Chain breaks: 1
        Number of residues, atoms: 448, 3641
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 19, 'TRANS': 428}
          Chain breaks: 1
        Number of residues, atoms: 2, 12
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 2}
          Link IDs: {'TRANS': 1}
          Chain breaks: 1
  Time building chain proxies: 4.17, per 1000 atoms: 0.57


================================== X-ray data =================================

F-obs:
  1yfs.mtz:FOBS_X,SIGFOBS_X

R-free flags:
  1yfs.mtz:R-free-flags

Miller array info: 1yfs.mtz:FOBS_X,SIGFOBS_X
Observation type: xray.amplitude
Type of data: double, size=57744
Type of sigmas: double, size=57744
Number of Miller indices: 57744
Anomalous flag: False
Unit cell: (173.026, 73.868, 73.999, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 5502
Resolution range: 36.934 2.08
Completeness in resolution range: 0.998616
Completeness with d_max=infinity: 0.998358

Number of F-obs in resolution range:                   57744
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  36.9340
                             d_min =   2.0800

Miller array info: 1yfs.mtz:R-free-flags
Observation type: None
Type of data: int, size=57744
Type of sigmas: None
Number of Miller indices: 57744
Anomalous flag: False
Unit cell: (173.026, 73.868, 73.999, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 5502
Resolution range: 36.934 2.08
Completeness in resolution range: 0.998616
Completeness with d_max=infinity: 0.998358

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 36.9398 -  4.4788 [6018/6088]  5396   622  10.3%
  bin  2:  4.4788 -  3.5559 [5846/5854]  5266   580   9.9%
  bin  3:  3.5559 -  3.1067 [5795/5797]  5177   618  10.7%
  bin  4:  3.1067 -  2.8227 [5765/5765]  5196   569   9.9%
  bin  5:  2.8227 -  2.6205 [5732/5732]  5144   588  10.3%
  bin  6:  2.6205 -  2.4660 [5712/5712]  5174   538   9.4%
  bin  7:  2.4660 -  2.3425 [5757/5757]  5152   605  10.5%
  bin  8:  2.3425 -  2.2406 [5662/5662]  5103   559   9.9%
  bin  9:  2.2406 -  2.1543 [5750/5750]  5176   574  10.0%
  bin 10:  2.1543 -  2.0800 [5707/5707]  5156   551   9.7%
                                overall 51940  5804  10.1%

========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.35 seconds
  Histogram of bond lengths:
        1.21 -     1.34: 2332
        1.34 -     1.46: 1257
        1.46 -     1.58: 3831
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  SER A 172 " - " C   SER A 172 " 1.525  1.496  0.029 2.27e+03 1.94e+00
  " N   ASN A  75 " - " CA  ASN A  75 " 1.458  1.436  0.022 2.77e+03 1.29e+00
  " CA  ILE A 353 " - " CB  ILE A 353 " 1.540  1.571 -0.031 1.37e+03 1.29e+00
  " N   ASN B 201 " - " CA  ASN B 201 " 1.458  1.436  0.022 2.77e+03 1.28e+00
  " CA  SER B 172 " - " C   SER B 172 " 1.525  1.502  0.023 2.27e+03 1.23e+00
  ... (remaining 7455 not shown)
  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 3292
        2.92 -     3.42: 7915
        3.42 -     3.91: 14030
        3.91 -     4.41: 16525
        4.41 -     4.90: 24800
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " N   GLU B 181 " - " OE1 GLU B 181 "  2.427 3.120
  " ND2 ASN A  95 " - " OG1 THR A 218 "  2.464 3.120
  " OE1 GLU B 174 " - " OH  TYR B 176 "  2.467 3.040
  " OH  TYR A  82 " - " OE2 GLU A 399 "  2.495 3.040
  " OH  TYR B 189 " - " O   THR B 389 "  2.524 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 66557 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 2226
       17.84 -    35.68: 330
       35.68 -    53.52: 156
       53.52 -    71.36: 42
       71.36 -    89.20: 28
  Dihedral angle restraints sorted by residual:
  " N   ARG B  56 "
  " CA  ARG B  56 "
  " CB  ARG B  56 "
  " CG  ARG B  56 "
      ideal   model   delta periodicty    weight residual
      60.00 -118.54   58.54     3       4.44e-03 1.52e+01
  " N   PRO B 330 "
  " CA  PRO B 330 "
  " CB  PRO B 330 "
  " CG  PRO B 330 "
      ideal   model   delta periodicty    weight residual
     -25.00   37.24   57.76     3       4.44e-03 1.48e+01
  " CA  HIS A 272 "
  " CB  HIS A 272 "
  " CG  HIS A 272 "
  " ND1 HIS A 272 "
      ideal   model   delta periodicty    weight residual
      90.00 -164.80   74.80     2       2.50e-03 1.40e+01
  ... (remaining 2779 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      24     15.96       2
   O    1354      7.97       2
   N    1232      6.97       2
   C    4684      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = False
group_occupancies      = False
group_anomalous        = False
size = 7294

n_use            =  7294
n_use_u_iso      =  7294
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  7294

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002.geo

CPU time processing inputs: 11.17


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 173.026001 73.86799622 73.99900055 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001.pdb"
    }
    xray_data {
      file_name = "1yfs.mtz"
      labels = "FOBS_X,SIGFOBS_X"
      r_free_flags {
        file_name = "1yfs.mtz"
        label = "R-free-flags"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "pdb1yfs_refine"
    serial = 2
  }
  main {
    ordered_solvent = True
    random_seed = 2772306
  }
  alpha_beta {
    interpolation = False
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2463   r_free= 0.2875   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.872105                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.9398 -  6.4519 0.97   1840  220 0.2661 0.2700      6.7956      6.7653|
|  2:  6.4519 -  5.1255 1.00   1790  203 0.2106 0.2361      6.3427      6.4673|
|  3:  5.1255 -  4.4788 1.00   1766  199 0.1829 0.2362      6.4156      6.5719|
|  4:  4.4788 -  4.0699 1.00   1773  186 0.1764 0.2152      6.4589      6.4944|
|  5:  4.0699 -  3.7785 1.00   1750  199 0.1934 0.2331      6.4109       6.531|
|  6:  3.7785 -  3.5559 1.00   1743  195 0.2047 0.2606      6.4009      6.5411|
|  7:  3.5559 -  3.3779 1.00   1713  204 0.2198 0.2624      6.3472      6.4424|
|  8:  3.3779 -  3.2310 1.00   1734  215 0.2255 0.2887      6.2695      6.3777|
|  9:  3.2310 -  3.1067 1.00   1730  199 0.2264 0.2918      6.1851       6.296|
| 10:  3.1067 -  2.9995 1.00   1727  189 0.2255 0.2628      6.0981      6.1846|
| 11:  2.9995 -  2.9058 1.00   1753  188 0.2300 0.2677      6.0086      6.1448|
| 12:  2.9058 -  2.8227 1.00   1716  192 0.2236 0.2580      5.9526      6.0756|
| 13:  2.8227 -  2.7485 1.00   1705  185 0.2303 0.2945      5.8839      6.0244|
| 14:  2.7485 -  2.6814 1.00   1758  187 0.2335 0.2944      5.8459      5.8999|
| 15:  2.6814 -  2.6205 1.00   1681  216 0.2063 0.2757      5.7308      5.8737|
| 16:  2.6205 -  2.5647 1.00   1746  186 0.2138 0.2816      5.6761      5.8076|
| 17:  2.5647 -  2.5134 1.00   1748  174 0.2200 0.2876      5.6565       5.826|
| 18:  2.5134 -  2.4660 1.00   1680  178 0.2176 0.2845      5.6183      5.6884|
| 19:  2.4660 -  2.4220 1.00   1745  202 0.2175 0.2998      5.5984      5.7809|
| 20:  2.4220 -  2.3809 1.00   1676  196 0.2186 0.2933        5.59      5.7312|
| 21:  2.3809 -  2.3425 1.00   1731  207 0.2282 0.2847      5.5896      5.6775|
| 22:  2.3425 -  2.3065 1.00   1689  201 0.2363 0.3157      5.5872      5.7482|
| 23:  2.3065 -  2.2726 1.00   1711  193 0.2322 0.3095      5.5606       5.688|
| 24:  2.2726 -  2.2406 1.00   1703  165 0.2274 0.3111      5.5201      5.6856|
| 25:  2.2406 -  2.2103 1.00   1789  182 0.2228 0.2746      5.4608      5.6166|
| 26:  2.2103 -  2.1816 1.00   1659  190 0.2212 0.2986       5.439      5.5578|
| 27:  2.1816 -  2.1543 1.00   1728  202 0.2315 0.3072      5.4618      5.5745|
| 28:  2.1543 -  2.1284 1.00   1722  172 0.2499 0.3324      5.4472      5.5838|
| 29:  2.1284 -  2.1036 1.00   1702  179 0.2262 0.2956       5.356      5.5438|
| 30:  2.1036 -  2.0800 1.00   1732  200 0.2263 0.2865      5.3046      5.4338|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 36.9398 -  6.4519  1840   220  0.83  22.45   0.59     0.63     108324.82|
|  2:  6.4519 -  5.1255  1790   203  0.85  21.82   0.70     0.67      64445.97|
|  3:  5.1255 -  4.4788  1766   199  0.90  17.27   0.79     0.74      65483.82|
|  4:  4.4788 -  4.0699  1773   186  0.91  16.18   0.87     0.79      64176.74|
|  5:  4.0699 -  3.7785  1750   199  0.89  18.04   0.92     0.87      66472.19|
|  6:  3.7785 -  3.5559  1743   195  0.88  20.00   0.95     0.90      70967.27|
|  7:  3.5559 -  3.3779  1713   204  0.85  22.91   0.97     0.89      66217.92|
|  8:  3.3779 -  3.2310  1734   215  0.82  25.33   0.97     0.90      63762.90|
|  9:  3.2310 -  3.1067  1730   199  0.82  25.08   0.95     0.88      53666.32|
| 10:  3.1067 -  2.9995  1727   189  0.84  23.39   0.93     0.87      42408.18|
| 11:  2.9995 -  2.9058  1753   188  0.84  23.51   0.91     0.82      33073.46|
| 12:  2.9058 -  2.8227  1716   192  0.84  23.51   0.92     0.87      32498.60|
| 13:  2.8227 -  2.7485  1705   185  0.82  25.71   0.88     0.80      29914.75|
| 14:  2.7485 -  2.6814  1758   187  0.81  26.17   0.89     0.78      26088.15|
| 15:  2.6814 -  2.6205  1681   216  0.86  22.44   0.88     0.81      21017.10|
| 16:  2.6205 -  2.5647  1746   186  0.86  22.42   0.88     0.82      18753.07|
| 17:  2.5647 -  2.5134  1748   174  0.84  23.86   0.88     0.82      18374.66|
| 18:  2.5134 -  2.4660  1680   178  0.84  23.69   0.87     0.81      17307.47|
| 19:  2.4660 -  2.4220  1745   202  0.84  24.39   0.88     0.82      17298.39|
| 20:  2.4220 -  2.3809  1676   196  0.82  25.98   0.91     0.81      17330.27|
| 21:  2.3809 -  2.3425  1731   207  0.82  26.24   0.89     0.79      17082.32|
| 22:  2.3425 -  2.3065  1689   201  0.80  27.75   0.89     0.79      17467.92|
| 23:  2.3065 -  2.2726  1711   193  0.81  27.29   0.91     0.80      16711.18|
| 24:  2.2726 -  2.2406  1703   165  0.81  26.91   0.93     0.82      15461.48|
| 25:  2.2406 -  2.2103  1789   182  0.82  25.59   0.91     0.81      12964.66|
| 26:  2.2103 -  2.1816  1659   190  0.82  25.54   0.93     0.82      12445.71|
| 27:  2.1816 -  2.1543  1728   202  0.80  28.15   0.92     0.79      13615.08|
| 28:  2.1543 -  2.1284  1722   172  0.76  31.02   0.92     0.80      14316.40|
| 29:  2.1284 -  2.1036  1702   179  0.79  28.59   0.93     0.84      12043.26|
| 30:  2.1036 -  2.0800  1732   200  0.83  25.34   0.89     0.79       9240.13|
|alpha:            min =        0.63 max =            0.92 mean =         0.81|
|beta:             min =     8688.90 max =       123749.52 mean =     34960.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.97 mean =        24.19|
|phase err.(test): min =        0.00 max =           89.72 mean =        24.63|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.505193              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.656  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.106052              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.564  (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.004:  4103 |   0.000 -   0.734:  7330 |  2.427 -  2.674:      136 |
| 0.004 - 0.008:  2040 |   0.734 -   1.467:  1816 |  2.674 -  2.922:     3156 |
| 0.008 - 0.011:   782 |   1.467 -   2.201:   577 |  2.922 -  3.169:     3608 |
| 0.011 - 0.015:   325 |   2.201 -   2.934:   171 |  3.169 -  3.416:     4307 |
| 0.015 - 0.019:   120 |   2.934 -   3.668:    84 |  3.416 -  3.664:     5705 |
| 0.019 - 0.023:    52 |   3.668 -   4.401:    33 |  3.664 -  3.911:     8325 |
| 0.023 - 0.026:    23 |   4.401 -   5.135:    15 |  3.911 -  4.158:     6664 |
| 0.026 - 0.030:     7 |   5.135 -   5.868:     9 |  4.158 -  4.405:     9861 |
| 0.030 - 0.034:     3 |   5.868 -   6.602:     8 |  4.405 -  4.653:    11442 |
| 0.034 - 0.038:     5 |   6.602 -   7.335:     1 |  4.653 -  4.900:    13358 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     7460 |   0.006    0.038  0.000 |       0.068 |              |
|     angle |    10044 |   0.902    7.335  0.000 |       0.157 |              |
| chirality |     1052 |   0.059    0.258  0.000 |       0.088 |        0.071 |
| planarity |     1306 |   0.004    0.039  0.000 |       0.097 |              |
|  dihedral |     2782 |  18.610   89.195  0.001 |       1.190 |              |
| nonbonded |     7460 |   4.117    4.900  2.427 |       0.099 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.114)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7294   0      5.16    68.82   21.78    None  None   None       |
|    all(noH): 7294   0      5.16    68.82   21.78    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7294   0      5.16    68.82   21.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.160 -  11.526:  395   |   5:    36.990 -  43.356:  194        |
|      1:    11.526 -  17.892: 2363   |   6:    43.356 -  49.722:  116        |
|      2:    17.892 -  24.258: 2478   |   7:    49.722 -  56.088:   80        |
|      3:    24.258 -  30.624: 1106   |   8:    56.088 -  62.454:   54        |
|      4:    30.624 -  36.990:  501   |   9:    62.454 -  68.820:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 1.00   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2463   r_free= 0.2875   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.872105                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2059   r_free= 0.2590   ksol= 0.24   Bsol= 16.21   scale= 0.900   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,0.60,1.14,0.00,0.00,0.00); trace/3= 0.13                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.833062                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.188996              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.374  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.108999              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.132  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2059      final r-factor (work) = 0.2033          |
| start r-factor (free) = 0.2590      final r-factor (free) = 0.2598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1023 = 8.19 * 0.50 * 5.8691 + 1.00 * 0.0712                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9479 = 8.19 * 0.50 * 5.8271 + 1.00 * 0.0890                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2033      final r-factor (work) = 0.2032          |
| start r-factor (free) = 0.2598      final r-factor (free) = 0.2602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6370 = 0.11 * 1.00 * 5.8271 + 1.00 * 0.0019                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6369 = 0.11 * 1.00 * 5.8249 + 1.00 * 0.0020                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.114)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7294   0      3.95    68.69   21.18    None  None   None       |
|    all(noH): 7294   0      3.95    68.69   21.18    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7294   0      3.95    68.69   21.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.952 -  10.426:  331   |   5:    36.320 -  42.794:  202        |
|      1:    10.426 -  16.900: 2218   |   6:    42.794 -  49.268:  108        |
|      2:    16.900 -  23.373: 2621   |   7:    49.268 -  55.741:   79        |
|      3:    23.373 -  29.847: 1152   |   8:    55.741 -  62.215:   55        |
|      4:    29.847 -  36.320:  520   |   9:    62.215 -  68.688:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2032   r_free= 0.2602   ksol= 0.24   Bsol= 16.21   scale= 0.890   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,0.60,1.14,0.00,0.00,0.00); trace/3= 0.13                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.826978                   |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 0      
  b_iso_min        =    None (limit = 1.00)
  b_iso_max        =    None (limit = 50.00)
  b_iso_mean       =    None             
  occupancy_min    =    None (limit = 0.10)
  occupancy_max    =    None (limit = 1.20)
  dist_sol_mol_min =    None (limit = 1.80)
  dist_sol_mol_max =    None (limit = 6.00)
Peak search:
   maximum allowed number of peaks:           7294
   number of peaks from mFobs-DFmodel map:  644
Filter by distance & map next to the model:
   mapped sites are within: 0.434 - 5.964 
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 521 from: 644
   mapped sites are within: 1.801 - 5.964 
2Fo-Fc map selection:
  number           = 352    
  b_iso_min        = 21.18   (limit = 1.00)
  b_iso_max        = 21.18   (limit = 50.00)
  b_iso_mean       = 21.18               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 1.92    (limit = 1.80)
  dist_sol_mol_max = 4.18    (limit = 6.00)

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1846   r_free= 0.2260   ksol= 0.23   Bsol= 21.27   scale= 0.906   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.28,2.19,2.71,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.727271                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.407073              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.642  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.081126              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.123  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1846      final r-factor (work) = 0.1763          |
| start r-factor (free) = 0.2260      final r-factor (free) = 0.2298          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7294 = 5.41 * 0.50 * 5.7841 + 1.00 * 0.0918                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5098 = 5.41 * 0.50 * 5.7076 + 1.00 * 0.0791                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1763      final r-factor (work) = 0.1722          |
| start r-factor (free) = 0.2298      final r-factor (free) = 0.2289          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4651 = 0.08 * 1.00 * 5.7076 + 1.00 * 0.0021                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4643 = 0.08 * 1.00 * 5.7007 + 1.00 * 0.0019                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.114)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7646   0      3.12    71.57   20.58    None  None   None       |
|    all(noH): 7646   0      3.12    71.57   20.58    None  None   None       |
|    Sol.    : 352    0      7.94    39.36   22.42    None  None   None       |
|    Mac.    : 7294   0      3.12    71.57   20.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.124 -   9.968:  319   |   5:    37.348 -  44.193:  174        |
|      1:     9.968 -  16.813: 2519   |   6:    44.193 -  51.038:   81        |
|      2:    16.813 -  23.658: 2783   |   7:    51.038 -  57.883:   75        |
|      3:    23.658 -  30.503: 1213   |   8:    57.883 -  64.728:   32        |
|      4:    30.503 -  37.348:  447   |   9:    64.728 -  71.573:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1722   r_free= 0.2289   ksol= 0.23   Bsol= 21.27   scale= 0.897   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.28,2.19,2.71,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.700155                   |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 352    
  b_iso_min        = 7.94    (limit = 1.00)
  b_iso_max        = 39.36   (limit = 50.00)
  b_iso_mean       = 22.42               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.33    (limit = 1.80)
  dist_sol_mol_max = 4.21    (limit = 6.00)
Peak search:
   maximum allowed number of peaks:           7294
   number of peaks from mFobs-DFmodel map:  620
Filter by distance & map next to the model:
   mapped sites are within: 0.121 - 5.982 
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 372 from: 620
   mapped sites are within: 1.803 - 5.982 
2Fo-Fc map selection:
  number           = 420    
  b_iso_min        = 7.94    (limit = 1.00)
  b_iso_max        = 39.36   (limit = 50.00)
  b_iso_mean       = 21.77               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 1.90    (limit = 1.80)
  dist_sol_mol_max = 5.17    (limit = 6.00)

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1741   r_free= 0.2225   ksol= 0.23   Bsol= 24.22   scale= 0.902   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,2.74,3.20,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.698846                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.117698              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.702  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.087301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.330  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1741      final r-factor (work) = 0.1699          |
| start r-factor (free) = 0.2225      final r-factor (free) = 0.2259          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5429 = 6.12 * 0.50 * 5.7086 + 1.00 * 0.0811                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4806 = 6.12 * 0.50 * 5.6874 + 1.00 * 0.0836                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1699      final r-factor (work) = 0.1675          |
| start r-factor (free) = 0.2259      final r-factor (free) = 0.2256          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4984 = 0.09 * 1.00 * 5.6874 + 1.00 * 0.0019                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4983 = 0.09 * 1.00 * 5.6833 + 1.00 * 0.0021                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.114)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7714   0      0.00    74.49   20.07    None  None   None       |
|    all(noH): 7714   0      0.00    74.49   20.07    None  None   None       |
|    Sol.    : 420    0      6.01    40.08   23.17    None  None   None       |
|    Mac.    : 7294   0      0.00    74.49   19.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.449:  106   |   5:    37.243 -  44.691:  183        |
|      1:     7.449 -  14.897: 2141   |   6:    44.691 -  52.140:   90        |
|      2:    14.897 -  22.346: 3150   |   7:    52.140 -  59.588:   68        |
|      3:    22.346 -  29.794: 1432   |   8:    59.588 -  67.037:   15        |
|      4:    29.794 -  37.243:  527   |   9:    67.037 -  74.485:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= ordered solvent: final clean up =======================

Start model:
  number           = 420    
  b_iso_min        = 6.01    (limit = 1.00)
  b_iso_max        = 40.08   (limit = 50.00)
  b_iso_mean       = 23.17               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.22    (limit = 1.80)
  dist_sol_mol_max = 5.06    (limit = 6.00)
2Fo-Fc map selection:
  number           = 399    
  b_iso_min        = 6.01    (limit = 1.00)
  b_iso_max        = 39.80   (limit = 50.00)
  b_iso_mean       = 22.79               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.22    (limit = 1.80)
  dist_sol_mol_max = 5.06    (limit = 6.00)

                         ----------X-ray data----------                        

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1689   r_free= 0.2262   ksol= 0.23   Bsol= 24.22   scale= 0.894   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,2.74,3.20,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.687978                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.9398 -  6.4519 0.97   1840  220 0.1217 0.1452      6.0821      6.1986|
|  2:  6.4519 -  5.1255 1.00   1790  203 0.1416 0.1816      5.9907      6.1944|
|  3:  5.1255 -  4.4788 1.00   1766  199 0.1301 0.1938      6.1274      6.3975|
|  4:  4.4788 -  4.0699 1.00   1773  186 0.1280 0.1745      6.1692      6.2717|
|  5:  4.0699 -  3.7785 1.00   1750  199 0.1459 0.1882      6.1746      6.3726|
|  6:  3.7785 -  3.5559 1.00   1743  195 0.1553 0.2074      6.1731      6.3537|
|  7:  3.5559 -  3.3779 1.00   1713  204 0.1699 0.1996      6.1285      6.2328|
|  8:  3.3779 -  3.2310 1.00   1734  215 0.1855 0.2528      6.0968      6.3162|
|  9:  3.2310 -  3.1067 1.00   1730  199 0.1797 0.2284      6.0012      6.1101|
| 10:  3.1067 -  2.9995 1.00   1727  189 0.1726 0.2320      5.9007      6.0546|
| 11:  2.9995 -  2.9058 1.00   1753  188 0.1822 0.2295      5.8224      6.0023|
| 12:  2.9058 -  2.8227 1.00   1716  192 0.1765 0.2189      5.7612      5.9304|
| 13:  2.8227 -  2.7485 1.00   1705  185 0.1872 0.2352      5.7127      5.8677|
| 14:  2.7485 -  2.6814 1.00   1758  187 0.1847 0.2595      5.6728      5.8161|
| 15:  2.6814 -  2.6205 1.00   1681  216 0.1672 0.2396      5.5977      5.7948|
| 16:  2.6205 -  2.5647 1.00   1746  186 0.1779 0.2565      5.5734      5.7403|
| 17:  2.5647 -  2.5134 1.00   1748  174 0.1808 0.2531      5.5309      5.6919|
| 18:  2.5134 -  2.4660 1.00   1680  178 0.1854 0.2679      5.5066      5.6616|
| 19:  2.4660 -  2.4220 1.00   1745  202 0.1920 0.2789      5.5102      5.7279|
| 20:  2.4220 -  2.3809 1.00   1676  196 0.1911 0.2615      5.4921      5.6472|
| 21:  2.3809 -  2.3425 1.00   1731  207 0.1887 0.2656      5.4645      5.5922|
| 22:  2.3425 -  2.3065 1.00   1689  201 0.1973 0.2939      5.4824       5.675|
| 23:  2.3065 -  2.2726 1.00   1711  193 0.2071 0.2738      5.4762       5.632|
| 24:  2.2726 -  2.2406 1.00   1703  165 0.2016 0.2862      5.4237      5.6323|
| 25:  2.2406 -  2.2103 1.00   1789  182 0.1862 0.2446      5.3369      5.4838|
| 26:  2.2103 -  2.1816 1.00   1659  190 0.1833 0.2640      5.3105      5.4784|
| 27:  2.1816 -  2.1543 1.00   1728  202 0.1925 0.2928      5.3342      5.5089|
| 28:  2.1543 -  2.1284 1.00   1722  172 0.2123 0.2859      5.3228      5.5054|
| 29:  2.1284 -  2.1036 1.00   1702  179 0.1848 0.2525      5.2063      5.4204|
| 30:  2.1036 -  2.0800 1.00   1732  200 0.1854 0.2540      5.1611      5.3398|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 36.9398 -  6.4519  1840   220  0.94  10.10   0.90     0.89      28603.08|
|  2:  6.4519 -  5.1255  1790   203  0.92  14.06   0.85     0.84      30933.90|
|  3:  5.1255 -  4.4788  1766   199  0.94  12.43   0.88     0.86      39811.64|
|  4:  4.4788 -  4.0699  1773   186  0.95  11.66   0.90     0.86      40769.29|
|  5:  4.0699 -  3.7785  1750   199  0.93  13.78   0.92     0.89      42898.20|
|  6:  3.7785 -  3.5559  1743   195  0.92  14.80   0.94     0.90      44039.71|
|  7:  3.5559 -  3.3779  1713   204  0.90  17.02   0.94     0.89      40469.74|
|  8:  3.3779 -  3.2310  1734   215  0.88  19.29   0.93     0.90      41286.71|
|  9:  3.2310 -  3.1067  1730   199  0.89  19.17   0.91     0.86      34887.70|
| 10:  3.1067 -  2.9995  1727   189  0.90  18.12   0.89     0.84      27850.64|
| 11:  2.9995 -  2.9058  1753   188  0.89  19.06   0.88     0.82      23785.96|
| 12:  2.9058 -  2.8227  1716   192  0.89  18.45   0.89     0.86      21602.70|
| 13:  2.8227 -  2.7485  1705   185  0.88  19.98   0.86     0.81      20012.00|
| 14:  2.7485 -  2.6814  1758   187  0.87  20.90   0.86     0.78      18475.26|
| 15:  2.6814 -  2.6205  1681   216  0.89  19.49   0.86     0.79      16776.95|
| 16:  2.6205 -  2.5647  1746   186  0.88  20.44   0.85     0.79      16052.74|
| 17:  2.5647 -  2.5134  1748   174  0.87  20.95   0.85     0.80      14912.40|
| 18:  2.5134 -  2.4660  1680   178  0.87  20.83   0.85     0.80      14169.48|
| 19:  2.4660 -  2.4220  1745   202  0.85  22.64   0.85     0.78      14905.99|
| 20:  2.4220 -  2.3809  1676   196  0.85  22.92   0.88     0.80      14294.12|
| 21:  2.3809 -  2.3425  1731   207  0.86  22.19   0.86     0.79      13431.61|
| 22:  2.3425 -  2.3065  1689   201  0.84  23.81   0.87     0.79      14193.03|
| 23:  2.3065 -  2.2726  1711   193  0.84  24.39   0.89     0.79      14033.12|
| 24:  2.2726 -  2.2406  1703   165  0.85  23.15   0.90     0.81      12277.71|
| 25:  2.2406 -  2.2103  1789   182  0.87  21.47   0.89     0.83      10056.16|
| 26:  2.2103 -  2.1816  1659   190  0.87  21.34   0.90     0.82       9587.03|
| 27:  2.1816 -  2.1543  1728   202  0.85  23.38   0.90     0.80      10398.74|
| 28:  2.1543 -  2.1284  1722   172  0.82  25.43   0.91     0.84      10570.62|
| 29:  2.1284 -  2.1036  1702   179  0.85  22.82   0.92     0.86       8442.11|
| 30:  2.1036 -  2.0800  1732   200  0.88  20.62   0.90     0.82       6778.58|
|alpha:            min =        0.77 max =            0.92 mean =         0.83|
|beta:             min =     6499.07 max =        44785.05 mean =     21978.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.76 mean =        19.44|
|phase err.(test): min =        0.00 max =           89.47 mean =        19.72|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1688   r_free= 0.2260   ksol= 0.23   Bsol= 28.26   scale= 0.902   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,0.53,0.95,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.687800                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1688   r_free= 0.2260   ksol= 0.23   Bsol= 28.26   scale= 0.902   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,0.53,0.95,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.687800                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.9398 -  6.4519 0.97   1840  220 0.1217 0.1453      6.0826      6.1989|
|  2:  6.4519 -  5.1255 1.00   1790  203 0.1418 0.1818      5.9913      6.1954|
|  3:  5.1255 -  4.4788 1.00   1766  199 0.1302 0.1938      6.1282       6.398|
|  4:  4.4788 -  4.0699 1.00   1773  186 0.1281 0.1747      6.1701       6.273|
|  5:  4.0699 -  3.7785 1.00   1750  199 0.1459 0.1884      6.1751      6.3732|
|  6:  3.7785 -  3.5559 1.00   1743  195 0.1553 0.2076      6.1733      6.3542|
|  7:  3.5559 -  3.3779 1.00   1713  204 0.1699 0.1997      6.1284      6.2326|
|  8:  3.3779 -  3.2310 1.00   1734  215 0.1855 0.2527      6.0967      6.3156|
|  9:  3.2310 -  3.1067 1.00   1730  199 0.1796 0.2284      6.0005      6.1098|
| 10:  3.1067 -  2.9995 1.00   1727  189 0.1725 0.2318      5.9002      6.0535|
| 11:  2.9995 -  2.9058 1.00   1753  188 0.1821 0.2293      5.8217      6.0017|
| 12:  2.9058 -  2.8227 1.00   1716  192 0.1764 0.2188      5.7606      5.9304|
| 13:  2.8227 -  2.7485 1.00   1705  185 0.1870 0.2350      5.7123      5.8673|
| 14:  2.7485 -  2.6814 1.00   1758  187 0.1846 0.2595      5.6722      5.8156|
| 15:  2.6814 -  2.6205 1.00   1681  216 0.1671 0.2395      5.5972      5.7945|
| 16:  2.6205 -  2.5647 1.00   1746  186 0.1778 0.2564       5.573        5.74|
| 17:  2.5647 -  2.5134 1.00   1748  174 0.1807 0.2530      5.5303      5.6912|
| 18:  2.5134 -  2.4660 1.00   1680  178 0.1853 0.2677      5.5061      5.6612|
| 19:  2.4660 -  2.4220 1.00   1745  202 0.1919 0.2788      5.5098      5.7276|
| 20:  2.4220 -  2.3809 1.00   1676  196 0.1911 0.2613      5.4919      5.6468|
| 21:  2.3809 -  2.3425 1.00   1731  207 0.1887 0.2656      5.4642      5.5921|
| 22:  2.3425 -  2.3065 1.00   1689  201 0.1972 0.2935      5.4819      5.6745|
| 23:  2.3065 -  2.2726 1.00   1711  193 0.2070 0.2736      5.4756      5.6314|
| 24:  2.2726 -  2.2406 1.00   1703  165 0.2016 0.2861      5.4235      5.6323|
| 25:  2.2406 -  2.2103 1.00   1789  182 0.1861 0.2448      5.3367      5.4839|
| 26:  2.2103 -  2.1816 1.00   1659  190 0.1831 0.2638      5.3103      5.4781|
| 27:  2.1816 -  2.1543 1.00   1728  202 0.1924 0.2928       5.334      5.5087|
| 28:  2.1543 -  2.1284 1.00   1722  172 0.2122 0.2858      5.3224       5.505|
| 29:  2.1284 -  2.1036 1.00   1702  179 0.1847 0.2523      5.2061      5.4202|
| 30:  2.1036 -  2.0800 1.00   1732  200 0.1854 0.2539      5.1611      5.3398|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 36.9398 -  6.4519  1840   220  0.94  10.10   0.91     0.89      28610.53|
|  2:  6.4519 -  5.1255  1790   203  0.92  14.07   0.85     0.84      30973.54|
|  3:  5.1255 -  4.4788  1766   199  0.94  12.44   0.88     0.86      39895.41|
|  4:  4.4788 -  4.0699  1773   186  0.95  11.67   0.90     0.86      40837.47|
|  5:  4.0699 -  3.7785  1750   199  0.93  13.79   0.93     0.90      42960.24|
|  6:  3.7785 -  3.5559  1743   195  0.92  14.81   0.95     0.91      44089.92|
|  7:  3.5559 -  3.3779  1713   204  0.90  17.03   0.95     0.90      40488.61|
|  8:  3.3779 -  3.2310  1734   215  0.88  19.29   0.94     0.91      41272.36|
|  9:  3.2310 -  3.1067  1730   199  0.89  19.16   0.92     0.87      34853.87|
| 10:  3.1067 -  2.9995  1727   189  0.90  18.10   0.90     0.85      27808.88|
| 11:  2.9995 -  2.9058  1753   188  0.89  19.04   0.89     0.83      23744.97|
| 12:  2.9058 -  2.8227  1716   192  0.89  18.45   0.90     0.87      21588.87|
| 13:  2.8227 -  2.7485  1705   185  0.88  19.98   0.88     0.82      20010.64|
| 14:  2.7485 -  2.6814  1758   187  0.87  20.89   0.87     0.79      18460.60|
| 15:  2.6814 -  2.6205  1681   216  0.89  19.49   0.87     0.80      16759.65|
| 16:  2.6205 -  2.5647  1746   186  0.88  20.43   0.86     0.80      16039.58|
| 17:  2.5647 -  2.5134  1748   174  0.87  20.94   0.87     0.81      14892.76|
| 18:  2.5134 -  2.4660  1680   178  0.87  20.82   0.87     0.81      14151.83|
| 19:  2.4660 -  2.4220  1745   202  0.85  22.64   0.87     0.79      14893.56|
| 20:  2.4220 -  2.3809  1676   196  0.85  22.91   0.90     0.82      14285.20|
| 21:  2.3809 -  2.3425  1731   207  0.86  22.19   0.88     0.81      13422.25|
| 22:  2.3425 -  2.3065  1689   201  0.84  23.79   0.89     0.81      14174.40|
| 23:  2.3065 -  2.2726  1711   193  0.84  24.36   0.91     0.81      14011.68|
| 24:  2.2726 -  2.2406  1703   165  0.85  23.14   0.92     0.83      12273.90|
| 25:  2.2406 -  2.2103  1789   182  0.87  21.47   0.91     0.85      10056.06|
| 26:  2.2103 -  2.1816  1659   190  0.87  21.33   0.92     0.84       9585.79|
| 27:  2.1816 -  2.1543  1728   202  0.85  23.37   0.92     0.82      10390.24|
| 28:  2.1543 -  2.1284  1722   172  0.83  25.41   0.94     0.86      10563.92|
| 29:  2.1284 -  2.1036  1702   179  0.85  22.81   0.95     0.88       8440.20|
| 30:  2.1036 -  2.0800  1732   200  0.88  20.61   0.92     0.84       6775.94|
|alpha:            min =        0.79 max =            0.93 mean =         0.84|
|beta:             min =     6496.14 max =        44839.63 mean =     21978.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.97 mean =        19.43|
|phase err.(test): min =        0.00 max =           89.60 mean =        19.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.114)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7693   0      2.68    77.16   22.72    None  None   None       |
|    all(noH): 7693   0      2.68    77.16   22.72    None  None   None       |
|    Sol.    : 399    0      8.68    42.48   25.47    None  None   None       |
|    Mac.    : 7294   0      2.68    77.16   22.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.678 -  10.127:  106   |   5:    39.921 -  47.369:  181        |
|      1:    10.127 -  17.575: 2141   |   6:    47.369 -  54.818:   90        |
|      2:    17.575 -  25.024: 3149   |   7:    54.818 -  62.266:   68        |
|      3:    25.024 -  32.472: 1424   |   8:    62.266 -  69.715:   15        |
|      4:    32.472 -  39.921:  517   |   9:    69.715 -  77.163:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_wat: ordered solvent update (add / remove)                            
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.2463 0.2875   5.872105e+00   5.998554e+00
   1_bss:  0.2059 0.2590   5.833062e+00   5.967237e+00
   1_xyz:  0.2033 0.2598   5.827590e+00   5.969340e+00
   1_adp:  0.2032 0.2602   5.826978e+00   5.969628e+00
   2_bss:  0.1846 0.2260   5.727271e+00   5.863957e+00
   2_xyz:  0.1763 0.2298   5.714326e+00   5.875738e+00
   2_adp:  0.1722 0.2289   5.700155e+00   5.869548e+00
   3_bss:  0.1741 0.2225   5.698846e+00   5.855128e+00
   3_xyz:  0.1699 0.2259   5.693257e+00   5.865422e+00
   3_adp:  0.1675 0.2256   5.684148e+00   5.862430e+00
   3_bss:  0.1688 0.2260   5.687800e+00   5.863183e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.238  16.214  -1.333   0.597   1.138   0.000   0.000   0.000
   1_xyz:  0.238  16.214  -1.333   0.597   1.138   0.000   0.000   0.000
   1_adp:  0.238  16.214  -1.333   0.597   1.138   0.000   0.000   0.000
   2_bss:  0.234  21.269   0.284   2.191   2.707   0.000   0.000   0.000
   2_xyz:  0.234  21.269   0.284   2.191   2.707   0.000   0.000   0.000
   2_adp:  0.234  21.269   0.284   2.191   2.707   0.000   0.000   0.000
   3_bss:  0.231  24.219   0.789   2.736   3.202   0.000   0.000   0.000
   3_xyz:  0.231  24.219   0.789   2.736   3.202   0.000   0.000   0.000
   3_adp:  0.231  24.219   0.789   2.736   3.202   0.000   0.000   0.000
   3_bss:  0.232  28.260  -1.480   0.526   0.954   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  24.233 0.8335  0.8112    35012.776
   1_bss:  23.382 0.8415  0.8228    29774.644
   1_xyz:  23.377 0.8416  0.8231    29973.439
   1_adp:  23.376 0.8416  0.8063    29990.983
   2_bss:  19.862 0.8759  0.8556    21916.773
   2_xyz:  20.059 0.8746  0.8479    22601.328
   2_adp:  19.807 0.8773  0.8327    22412.763
   3_bss:  19.250 0.8828  0.8471    21508.859
   3_xyz:  19.493 0.8807  0.8448    22158.927
   3_adp:  19.417 0.8815  0.8301    22013.849
   3_bss:  19.462 0.8810  0.8432    21996.794
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   0.902  0.006  0.059 18.610  0.004  4.117   7.1208e-02
   1_bss:   0.902  0.006  0.059 18.610  0.004  4.117   7.1208e-02
   1_xyz:   1.076  0.008  0.069 18.931  0.005  4.117   8.9040e-02
   1_adp:   1.076  0.008  0.069 18.931  0.005  4.117   8.9040e-02
   2_bss:   1.076  0.008  0.069 18.931  0.005  4.109   9.1814e-02
   2_xyz:   1.015  0.008  0.065 18.793  0.004  4.113   7.9111e-02
   2_adp:   1.015  0.008  0.065 18.793  0.004  4.113   7.9111e-02
   3_bss:   1.015  0.008  0.065 18.793  0.004  4.109   8.1115e-02
   3_xyz:   1.054  0.008  0.068 18.919  0.005  4.109   8.3624e-02
   3_adp:   1.054  0.008  0.068 18.919  0.005  4.109   8.3624e-02
   3_bss:   1.054  0.008  0.068 18.919  0.005  4.109   8.3700e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   7.335  0.038  0.258 89.195  0.039  2.427   2.6571e-02
   1_bss:   7.335  0.038  0.258 89.195  0.039  2.427   2.6571e-02
   1_xyz:   8.268  0.053  0.266 88.868  0.044  2.364   3.6752e-02
   1_adp:   8.268  0.053  0.266 88.868  0.044  2.364   3.6752e-02
   2_bss:   8.268  0.053  0.266 88.868  0.044  1.923   3.4970e-02
   2_xyz:   8.986  0.053  0.248 89.982  0.038  2.330   3.5285e-02
   2_adp:   8.986  0.053  0.248 89.982  0.038  2.330   3.5285e-02
   3_bss:   8.986  0.053  0.248 89.982  0.038  1.899   3.5149e-02
   3_xyz:   8.451  0.059  0.262 89.096  0.038  2.217   3.4414e-02
   3_adp:   8.451  0.059  0.262 89.096  0.038  2.217   3.4414e-02
   3_bss:   8.451  0.059  0.262 89.096  0.038  2.217   3.4494e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  68.82   5.16  21.78  68.69   3.95  21.18  21.18  21.18  21.18
   1_bss:  68.82   5.16  21.78  68.69   3.95  21.18  21.18  21.18  21.18
   1_xyz:  68.82   5.16  21.78  71.57   3.12  20.49  39.36   7.94  22.42
   1_adp:  68.69   3.95  21.18  71.57   3.12  20.49  39.36   7.94  21.77
   2_bss:  68.69   3.95  21.18  71.57   3.12  20.49  39.36   7.94  21.77
   2_xyz:  68.69   3.95  21.18  74.49   0.00  19.90  40.08   6.01  23.17
   2_adp:  71.57   3.12  20.58  77.16   2.68  22.57  42.48   8.68  25.47
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.342    0.001    0.022
   1_adp:    0.342    0.001    0.022
   2_bss:    0.342    0.001    0.022
   2_xyz:    0.430    0.001    0.059
   2_adp:    0.430    0.001    0.059
   3_bss:    0.430    0.001    0.059
   3_xyz:    0.675    0.002    0.072
   3_adp:    0.675    0.002    0.072
   3_bss:    0.675    0.002    0.072
------------------------------------------------------------------------
 stage  number of ordered solvent
     0    :                0
     1_bss:                0
     1_xyz:                0
     1_adp:                0
     2_bss:              352
     2_xyz:              352
     2_adp:              352
     3_bss:              420
     3_xyz:              420
     3_adp:              420
     3_bss:              399
------------------------------------------------------------------------

CPU time actual refinement: 468.46


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002.pdb
n_use            =  7693
n_use_u_iso      =  7693
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  7693
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  7693

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_003.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 468.30 
  Macro-tasks:
    bulk solvent and scale       = 110.18 
    individual site refinement   = 186.36 
    weights calculation          = 45.25  
    collect and process          = 12.27  
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 354.22 
  Micro-tasks:
    mask                            = 4.06   
    f_calc                          = 80.78  
    alpha_beta                      = 21.43  
    target                          = 2.24   
    gradients_wrt_atomic_parameters = 110.55 
    fmodel                         = 13.37  
    r_factors                      = 0.68   
    phase_errors                   = 20.03  
    foms                           = 0.47   
    TOTAL for micro-tasks          = 253.61 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.417 micro seconds
Total CPU time: 8.18 minutes
from_scatterers_fft:    221 calls, 80.07 s
gradients_fft:          190 calls, 91.66 s

=========================== phenix.refine: finished ===========================

# Date 2007-12-01 Time 01:05:20 PST -0800 (1196499920.48 s)
Start R-work = 0.2463, R-free = 0.2875 (no bulk solvent and anisotropic scale)
Final R-work = 0.2046, R-free = 0.2487 (no bulk solvent and anisotropic scale)

Start R-work = 0.2059, R-free = 0.2590
Final R-work = 0.1688, R-free = 0.2260