# Date 2007-12-01 Time 00:47:33 PST -0800 (1196498853.48 s)
#phil __OFF__

Command line arguments: "1yfs.mtz" "pdb1yfs.ent"

HOST = rosie.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12783

-------------------------------------------------------------------------------
  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.

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)

pdb1yfs.ent
  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: 4.18, 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%

No array of experimental phases found.


========================== 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: 0.34 seconds
  Histogram of bond lengths:
        1.22 -     1.34: 2384
        1.34 -     1.47: 1786
        1.47 -     1.59: 3250
        1.59 -     1.72: 0
        1.72 -     1.84: 40
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SD  MET A  92 " - " CE  MET A  92 " 1.791  1.844 -0.053 1.60e+03 4.56e+00
  " N   ALA  2500 " - " CA  ALA  2500 " 1.458  1.497 -0.039 2.77e+03 4.21e+00
  " SD  MET B 327 " - " CE  MET B 327 " 1.791  1.741  0.050 1.60e+03 3.99e+00
  " N   ALA  1500 " - " CA  ALA  1500 " 1.458  1.490 -0.032 2.77e+03 2.92e+00
  " SD  MET A 220 " - " CE  MET A 220 " 1.791  1.831 -0.040 1.60e+03 2.60e+00
  ... (remaining 7455 not shown)
  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 3074
        2.90 -     3.40: 7848
        3.40 -     3.90: 14054
        3.90 -     4.40: 16682
        4.40 -     4.90: 25222
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " ND2 ASN A  95 " - " OG1 THR A 218 "  2.397 3.120
  " OE1 GLU A 174 " - " OH  TYR A 176 "  2.471 3.040
  " N   GLU A 333 " - " OE1 GLU A 333 "  2.487 3.120
  " OE1 GLU B 174 " - " OH  TYR B 176 "  2.507 3.040
  " OH  TYR A  82 " - " OE2 GLU A 399 "  2.521 3.040
  ... (remaining 66875 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 2278
       17.82 -    35.64: 231
       35.64 -    53.46: 168
       53.46 -    71.28: 77
       71.28 -    89.11: 28
  Dihedral angle restraints sorted by residual:
  " CA  HIS A 272 "
  " CB  HIS A 272 "
  " CG  HIS A 272 "
  " ND1 HIS A 272 "
      ideal   model   delta periodicty    weight residual
      90.00 -172.17   82.17     2       2.50e-03 1.69e+01
  " N   ARG B  56 "
  " CA  ARG B  56 "
  " CB  ARG B  56 "
  " CG  ARG B  56 "
      ideal   model   delta periodicty    weight residual
      60.00 -120.00   60.00     3       4.44e-03 1.60e+01
  " N   PRO A 437 "
  " CA  PRO A 437 "
  " CB  PRO A 437 "
  " CG  PRO A 437 "
      ideal   model   delta periodicty    weight residual
     -25.00   34.69  -59.69     3       4.44e-03 1.58e+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_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001.geo

CPU time processing inputs: 11.23


============================ 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.ent"
    }
    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 = 1
  }
}
#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= 0.2588   r_free= 0.2832   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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: 5.906458                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.2705 0.2711      6.8153      6.7754|
|  2:  6.4519 -  5.1255 1.00   1790  203 0.2239 0.2287      6.3983      6.4626|
|  3:  5.1255 -  4.4788 1.00   1766  199 0.1947 0.2327      6.4556      6.5636|
|  4:  4.4788 -  4.0699 1.00   1773  186 0.1845 0.2136      6.4731      6.4685|
|  5:  4.0699 -  3.7785 1.00   1750  199 0.2067 0.2332      6.4555      6.5348|
|  6:  3.7785 -  3.5559 1.00   1743  195 0.2165 0.2502      6.4207      6.5116|
|  7:  3.5559 -  3.3779 1.00   1713  204 0.2307 0.2621      6.3681      6.4383|
|  8:  3.3779 -  3.2310 1.00   1734  215 0.2324 0.2725      6.2722       6.361|
|  9:  3.2310 -  3.1067 1.00   1730  199 0.2381 0.2932       6.202      6.2913|
| 10:  3.1067 -  2.9995 1.00   1727  189 0.2350 0.2494       6.117      6.1536|
| 11:  2.9995 -  2.9058 1.00   1753  188 0.2479 0.2703      6.0417      6.1309|
| 12:  2.9058 -  2.8227 1.00   1716  192 0.2424 0.2640      5.9822      6.0577|
| 13:  2.8227 -  2.7485 1.00   1705  185 0.2460 0.2926       5.903      6.0169|
| 14:  2.7485 -  2.6814 1.00   1758  187 0.2444 0.2755      5.8531      5.8662|
| 15:  2.6814 -  2.6205 1.00   1681  216 0.2246 0.2675      5.7678      5.8589|
| 16:  2.6205 -  2.5647 1.00   1746  186 0.2418 0.2827       5.738      5.8014|
| 17:  2.5647 -  2.5134 1.00   1748  174 0.2384 0.2841      5.7022      5.8233|
| 18:  2.5134 -  2.4660 1.00   1680  178 0.2421 0.2848      5.6655      5.6938|
| 19:  2.4660 -  2.4220 1.00   1745  202 0.2472 0.2850      5.6539      5.7563|
| 20:  2.4220 -  2.3809 1.00   1676  196 0.2444 0.2894      5.6269      5.7348|
| 21:  2.3809 -  2.3425 1.00   1731  207 0.2451 0.2732      5.6181      5.6573|
| 22:  2.3425 -  2.3065 1.00   1689  201 0.2552 0.3104      5.6172      5.7384|
| 23:  2.3065 -  2.2726 1.00   1711  193 0.2558 0.3119      5.5949      5.6889|
| 24:  2.2726 -  2.2406 1.00   1703  165 0.2546 0.3145      5.5734      5.6945|
| 25:  2.2406 -  2.2103 1.00   1789  182 0.2495 0.2598      5.5067      5.5514|
| 26:  2.2103 -  2.1816 1.00   1659  190 0.2471 0.2846      5.4765      5.5316|
| 27:  2.1816 -  2.1543 1.00   1728  202 0.2588 0.3035      5.4937      5.5732|
| 28:  2.1543 -  2.1284 1.00   1722  172 0.2695 0.3301      5.4701      5.5756|
| 29:  2.1284 -  2.1036 1.00   1702  179 0.2531 0.2938      5.4022       5.538|
| 30:  2.1036 -  2.0800 1.00   1732  200 0.2563 0.3073      5.3787      5.4582|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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  0.82  23.25   0.58     0.63     113202.37|
|  2:  6.4519 -  5.1255  1790   203  0.83  23.69   0.70     0.67      73607.50|
|  3:  5.1255 -  4.4788  1766   199  0.90  17.37   0.79     0.73      63302.67|
|  4:  4.4788 -  4.0699  1773   186  0.91  15.93   0.87     0.80      63121.34|
|  5:  4.0699 -  3.7785  1750   199  0.89  18.06   0.91     0.85      64694.52|
|  6:  3.7785 -  3.5559  1743   195  0.88  19.32   0.94     0.89      66029.67|
|  7:  3.5559 -  3.3779  1713   204  0.85  22.50   0.95     0.89      64121.89|
|  8:  3.3779 -  3.2310  1734   215  0.83  24.63   0.95     0.89      60018.90|
|  9:  3.2310 -  3.1067  1730   199  0.83  24.35   0.94     0.88      51350.77|
| 10:  3.1067 -  2.9995  1727   189  0.85  22.99   0.92     0.85      41056.30|
| 11:  2.9995 -  2.9058  1753   188  0.84  23.69   0.90     0.85      34201.59|
| 12:  2.9058 -  2.8227  1716   192  0.85  23.15   0.90     0.84      30255.74|
| 13:  2.8227 -  2.7485  1705   185  0.83  24.53   0.86     0.81      28225.06|
| 14:  2.7485 -  2.6814  1758   187  0.83  24.71   0.88     0.79      24269.07|
| 15:  2.6814 -  2.6205  1681   216  0.86  22.21   0.87     0.80      20218.45|
| 16:  2.6205 -  2.5647  1746   186  0.85  22.82   0.86     0.81      18751.13|
| 17:  2.5647 -  2.5134  1748   174  0.84  23.95   0.86     0.80      18199.69|
| 18:  2.5134 -  2.4660  1680   178  0.84  24.30   0.86     0.80      17632.36|
| 19:  2.4660 -  2.4220  1745   202  0.83  24.85   0.86     0.80      17134.84|
| 20:  2.4220 -  2.3809  1676   196  0.82  25.60   0.88     0.80      16458.46|
| 21:  2.3809 -  2.3425  1731   207  0.82  25.69   0.87     0.79      16393.98|
| 22:  2.3425 -  2.3065  1689   201  0.80  27.46   0.88     0.78      16815.56|
| 23:  2.3065 -  2.2726  1711   193  0.80  27.40   0.89     0.79      16478.93|
| 24:  2.2726 -  2.2406  1703   165  0.81  26.62   0.91     0.80      14690.23|
| 25:  2.2406 -  2.2103  1789   182  0.83  24.59   0.88     0.81      12145.88|
| 26:  2.2103 -  2.1816  1659   190  0.83  24.56   0.91     0.81      11441.37|
| 27:  2.1816 -  2.1543  1728   202  0.81  26.77   0.90     0.80      12702.07|
| 28:  2.1543 -  2.1284  1722   172  0.77  30.29   0.89     0.80      13580.98|
| 29:  2.1284 -  2.1036  1702   179  0.78  29.71   0.90     0.79      12317.81|
| 30:  2.1036 -  2.0800  1732   200  0.81  27.19   0.88     0.76       9941.65|
|alpha:            min =        0.62 max =            0.89 mean =         0.80|
|beta:             min =     9392.61 max =       123763.00 mean =     34429.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.99 mean =        24.05|
|phase err.(test): min =        0.00 max =           89.70 mean =        24.20|
|-----------------------------------------------------------------------------|

============================== 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 = 4.555836              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.320  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.105829              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.326  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.005:  5450 |   0.000 -   1.282:  8627 |  2.397 -  2.647:      104 |
| 0.005 - 0.011:  1446 |   1.282 -   2.565:  1025 |  2.647 -  2.898:     2970 |
| 0.011 - 0.016:   428 |   2.565 -   3.847:   232 |  2.898 -  3.148:     3732 |
| 0.016 - 0.021:    94 |   3.847 -   5.130:   108 |  3.148 -  3.398:     4116 |
| 0.021 - 0.027:    26 |   5.130 -   6.412:    36 |  3.398 -  3.648:     5740 |
| 0.027 - 0.032:     7 |   6.412 -   7.695:     5 |  3.648 -  3.899:     8314 |
| 0.032 - 0.037:     5 |   7.695 -   8.977:     5 |  3.899 -  4.149:     6870 |
| 0.037 - 0.043:     2 |   8.977 -  10.259:     4 |  4.149 -  4.399:     9812 |
| 0.043 - 0.048:     0 |  10.259 -  11.542:     0 |  4.399 -  4.650:    11798 |
| 0.048 - 0.053:     2 |  11.542 -  12.824:     2 |  4.650 -  4.900:    13424 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     7460 |   0.006    0.053  0.000 |       0.060 |              |
|     angle |    10044 |   1.107   12.824  0.000 |       0.219 |              |
| chirality |     1052 |   0.083    0.310  0.000 |       0.172 |        0.077 |
| planarity |     1306 |   0.006    0.044  0.000 |       0.339 |              |
|  dihedral |     2782 |  19.352   89.106  0.001 |       1.006 |              |
| nonbonded |     7460 |   4.114    4.900  2.397 |       0.109 |              |
|-----------------------------------------------------------------------------|

|-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      6.00    55.11   21.13    None  None   None       |
|    all(noH): 7294   0      6.00    55.11   21.13    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7294   0      6.00    55.11   21.13    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:     6.000 -  10.911:  411   |   5:    30.555 -  35.466:  469        |
|      1:    10.911 -  15.822: 1470   |   6:    35.466 -  40.377:  207        |
|      2:    15.822 -  20.733: 2220   |   7:    40.377 -  45.288:   87        |
|      3:    20.733 -  25.644: 1466   |   8:    45.288 -  50.199:   89        |
|      4:    25.644 -  30.555:  842   |   9:    50.199 -  55.110:   33        |
|                               =>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= 0.2588   r_free= 0.2832   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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: 5.906458                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2228   r_free= 0.2556   ksol= 0.24   Bsol= 22.01   scale= 0.895   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.93,1.37,0.00,0.00,0.00); trace/3= 0.39                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.873292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.330727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.047  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.106783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.919  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2228      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.2556      final r-factor (free) = 0.2580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8641 = 4.33 * 0.50 * 5.9054 + 1.00 * 0.0769                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7391 = 4.33 * 0.50 * 5.8520 + 1.00 * 0.0675                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2149      final r-factor (work) = 0.2087          |
| start r-factor (free) = 0.2580      final r-factor (free) = 0.2591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6264 = 0.11 * 1.00 * 5.8520 + 1.00 * 0.0015                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6250 = 0.11 * 1.00 * 5.8345 + 1.00 * 0.0020                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-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      3.45    66.55   20.78    None  None   None       |
|    all(noH): 7294   0      3.45    66.55   20.78    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7294   0      3.45    66.55   20.78    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:     3.454 -   9.763:  284   |   5:    35.001 -  41.310:  212        |
|      1:     9.763 -  16.073: 2021   |   6:    41.310 -  47.620:  130        |
|      2:    16.073 -  22.382: 2655   |   7:    47.620 -  53.929:   90        |
|      3:    22.382 -  28.691: 1266   |   8:    53.929 -  60.239:   43        |
|      4:    28.691 -  35.001:  589   |   9:    60.239 -  66.548:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2087   r_free= 0.2591   ksol= 0.24   Bsol= 22.01   scale= 0.888   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.93,1.37,0.00,0.00,0.00); trace/3= 0.39                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.837085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2085   r_free= 0.2587   ksol= 0.24   Bsol= 20.00   scale= 0.902   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,1.62,2.13,0.00,0.00,0.00); trace/3= 1.13                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.837293                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.330251              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.774  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.109303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.844  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2085      final r-factor (work) = 0.2054          |
| start r-factor (free) = 0.2587      final r-factor (free) = 0.2596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5434 = 6.33 * 0.50 * 5.8373 + 1.00 * 0.0675                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5284 = 6.33 * 0.50 * 5.8299 + 1.00 * 0.0761                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2054      final r-factor (work) = 0.2054          |
| start r-factor (free) = 0.2596      final r-factor (free) = 0.2597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6392 = 0.11 * 1.00 * 5.8299 + 1.00 * 0.0020                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6392 = 0.11 * 1.00 * 5.8290 + 1.00 * 0.0020                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-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      3.13    66.57   20.21    None  None   None       |
|    all(noH): 7294   0      3.13    66.57   20.21    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7294   0      3.13    66.57   20.21    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:     3.131 -   9.475:  315   |   5:    34.852 -  41.196:  204        |
|      1:     9.475 -  15.819: 2161   |   6:    41.196 -  47.540:  127        |
|      2:    15.819 -  22.164: 2629   |   7:    47.540 -  53.884:   84        |
|      3:    22.164 -  28.508: 1178   |   8:    53.884 -  60.228:   49        |
|      4:    28.508 -  34.852:  541   |   9:    60.228 -  66.572:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2054   r_free= 0.2597   ksol= 0.24   Bsol= 20.00   scale= 0.892   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,1.62,2.13,0.00,0.00,0.00); trace/3= 1.13                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.831102                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2053   r_free= 0.2595   ksol= 0.24   Bsol= 12.72   scale= 0.899   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.10,2.04,2.58,0.00,0.00,0.00); trace/3= 1.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.832288                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.659642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.620  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.114828              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.908  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2053      final r-factor (work) = 0.2056          |
| start r-factor (free) = 0.2595      final r-factor (free) = 0.2601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5758 = 5.66 * 0.50 * 5.8306 + 1.00 * 0.0761                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5770 = 5.66 * 0.50 * 5.8329 + 1.00 * 0.0709                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2056      final r-factor (work) = 0.2058          |
| start r-factor (free) = 0.2601      final r-factor (free) = 0.2602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6718 = 0.11 * 1.00 * 5.8329 + 1.00 * 0.0020                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6717 = 0.11 * 1.00 * 5.8315 + 1.00 * 0.0021                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-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      3.03    66.69   19.66    None  None   None       |
|    all(noH): 7294   0      3.03    66.69   19.66    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7294   0      3.03    66.69   19.66    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:     3.034 -   9.400:  396   |   5:    34.862 -  41.227:  194        |
|      1:     9.400 -  15.765: 2360   |   6:    41.227 -  47.593:  116        |
|      2:    15.765 -  22.131: 2481   |   7:    47.593 -  53.959:   80        |
|      3:    22.131 -  28.496: 1105   |   8:    53.959 -  60.324:   54        |
|      4:    28.496 -  34.862:  501   |   9:    60.324 -  66.690:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2058   r_free= 0.2602   ksol= 0.24   Bsol= 12.72   scale= 0.888   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.10,2.04,2.58,0.00,0.00,0.00); trace/3= 1.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.833195                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.1488 0.1835      6.2703      6.4029|
|  2:  6.4519 -  5.1255 1.00   1790  203 0.1679 0.2019      6.1436      6.3023|
|  3:  5.1255 -  4.4788 1.00   1766  199 0.1568 0.2077      6.2765      6.4845|
|  4:  4.4788 -  4.0699 1.00   1773  186 0.1557 0.2006      6.3386       6.405|
|  5:  4.0699 -  3.7785 1.00   1750  199 0.1767 0.2107      6.3256      6.4516|
|  6:  3.7785 -  3.5559 1.00   1743  195 0.1954 0.2424      6.3527       6.488|
|  7:  3.5559 -  3.3779 1.00   1713  204 0.2129 0.2502       6.315      6.4092|
|  8:  3.3779 -  3.2310 1.00   1734  215 0.2211 0.2862       6.248      6.3764|
|  9:  3.2310 -  3.1067 1.00   1730  199 0.2246 0.2898      6.1795      6.2827|
| 10:  3.1067 -  2.9995 1.00   1727  189 0.2221 0.2702      6.0921      6.2002|
| 11:  2.9995 -  2.9058 1.00   1753  188 0.2310 0.2710      6.0134      6.1486|
| 12:  2.9058 -  2.8227 1.00   1716  192 0.2235 0.2560       5.951      6.0574|
| 13:  2.8227 -  2.7485 1.00   1705  185 0.2320 0.2962      5.8837      6.0286|
| 14:  2.7485 -  2.6814 1.00   1758  187 0.2362 0.2952      5.8543      5.9051|
| 15:  2.6814 -  2.6205 1.00   1681  216 0.2085 0.2756      5.7375      5.8764|
| 16:  2.6205 -  2.5647 1.00   1746  186 0.2126 0.2889      5.6806      5.8242|
| 17:  2.5647 -  2.5134 1.00   1748  174 0.2205 0.2889      5.6651       5.826|
| 18:  2.5134 -  2.4660 1.00   1680  178 0.2198 0.2928      5.6289      5.7019|
| 19:  2.4660 -  2.4220 1.00   1745  202 0.2187 0.2980       5.604      5.7861|
| 20:  2.4220 -  2.3809 1.00   1676  196 0.2208 0.2892      5.5954      5.7275|
| 21:  2.3809 -  2.3425 1.00   1731  207 0.2268 0.2956      5.5916      5.6916|
| 22:  2.3425 -  2.3065 1.00   1689  201 0.2375 0.3143      5.5934      5.7444|
| 23:  2.3065 -  2.2726 1.00   1711  193 0.2359 0.3118      5.5661      5.6927|
| 24:  2.2726 -  2.2406 1.00   1703  165 0.2255 0.3144      5.5209       5.684|
| 25:  2.2406 -  2.2103 1.00   1789  182 0.2205 0.2761      5.4591      5.6241|
| 26:  2.2103 -  2.1816 1.00   1659  190 0.2224 0.3029      5.4437      5.5596|
| 27:  2.1816 -  2.1543 1.00   1728  202 0.2320 0.3074       5.462      5.5767|
| 28:  2.1543 -  2.1284 1.00   1722  172 0.2481 0.3246      5.4455      5.5745|
| 29:  2.1284 -  2.1036 1.00   1702  179 0.2243 0.3003       5.353      5.5505|
| 30:  2.1036 -  2.0800 1.00   1732  200 0.2224 0.2853      5.3012      5.4311|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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  0.92  13.07   0.91     0.89      43861.46|
|  2:  6.4519 -  5.1255  1790   203  0.90  16.59   0.82     0.82      41679.88|
|  3:  5.1255 -  4.4788  1766   199  0.92  14.22   0.86     0.83      49298.13|
|  4:  4.4788 -  4.0699  1773   186  0.93  14.08   0.89     0.83      52505.54|
|  5:  4.0699 -  3.7785  1750   199  0.91  16.30   0.92     0.88      55796.74|
|  6:  3.7785 -  3.5559  1743   195  0.89  18.22   0.95     0.89      60893.25|
|  7:  3.5559 -  3.3779  1713   204  0.86  21.59   0.95     0.88      59478.26|
|  8:  3.3779 -  3.2310  1734   215  0.83  24.32   0.95     0.89      59829.49|
|  9:  3.2310 -  3.1067  1730   199  0.83  24.73   0.92     0.85      52125.19|
| 10:  3.1067 -  2.9995  1727   189  0.84  23.40   0.90     0.84      42291.22|
| 11:  2.9995 -  2.9058  1753   188  0.84  23.87   0.88     0.79      33517.44|
| 12:  2.9058 -  2.8227  1716   192  0.84  23.35   0.88     0.83      32239.62|
| 13:  2.8227 -  2.7485  1705   185  0.82  25.48   0.85     0.77      29517.11|
| 14:  2.7485 -  2.6814  1758   187  0.81  26.36   0.86     0.75      26587.35|
| 15:  2.6814 -  2.6205  1681   216  0.85  22.74   0.85     0.77      21452.01|
| 16:  2.6205 -  2.5647  1746   186  0.85  22.78   0.84     0.78      19223.34|
| 17:  2.5647 -  2.5134  1748   174  0.83  24.40   0.84     0.78      19001.77|
| 18:  2.5134 -  2.4660  1680   178  0.84  24.26   0.84     0.76      17945.64|
| 19:  2.4660 -  2.4220  1745   202  0.83  24.78   0.84     0.78      17720.50|
| 20:  2.4220 -  2.3809  1676   196  0.82  26.15   0.86     0.77      17501.46|
| 21:  2.3809 -  2.3425  1731   207  0.81  26.52   0.85     0.75      17313.55|
| 22:  2.3425 -  2.3065  1689   201  0.80  28.01   0.85     0.76      17755.43|
| 23:  2.3065 -  2.2726  1711   193  0.80  27.54   0.87     0.76      16803.92|
| 24:  2.2726 -  2.2406  1703   165  0.81  26.98   0.89     0.79      15657.47|
| 25:  2.2406 -  2.2103  1789   182  0.82  25.57   0.87     0.78      13124.13|
| 26:  2.2103 -  2.1816  1659   190  0.82  25.65   0.89     0.78      12512.48|
| 27:  2.1816 -  2.1543  1728   202  0.80  27.98   0.88     0.76      13570.23|
| 28:  2.1543 -  2.1284  1722   172  0.76  30.89   0.88     0.77      14352.09|
| 29:  2.1284 -  2.1036  1702   179  0.79  28.42   0.89     0.80      11946.65|
| 30:  2.1036 -  2.0800  1732   200  0.83  25.35   0.86     0.75       9241.46|
|alpha:            min =        0.73 max =            0.92 mean =         0.80|
|beta:             min =     8675.88 max =        61643.72 mean =     29969.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.95 mean =        23.39|
|phase err.(test): min =        0.00 max =           89.56 mean =        23.87|
|-----------------------------------------------------------------------------|

====================== 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= 16.67   scale= 0.898   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,0.46,1.00,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.832923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.2059   r_free= 0.2590   ksol= 0.24   Bsol= 16.67   scale= 0.898   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,0.46,1.00,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.832923                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| 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 0.1526 0.1793      6.2827      6.3885|
|  2:  6.4519 -  5.1255 1.00   1790  203 0.1692 0.1972      6.1421      6.2858|
|  3:  5.1255 -  4.4788 1.00   1766  199 0.1584 0.2069      6.2794      6.4805|
|  4:  4.4788 -  4.0699 1.00   1773  186 0.1566 0.2000      6.3398      6.3981|
|  5:  4.0699 -  3.7785 1.00   1750  199 0.1768 0.2127      6.3277      6.4584|
|  6:  3.7785 -  3.5559 1.00   1743  195 0.1956 0.2435      6.3524      6.4868|
|  7:  3.5559 -  3.3779 1.00   1713  204 0.2137 0.2493      6.3149      6.4052|
|  8:  3.3779 -  3.2310 1.00   1734  215 0.2203 0.2868      6.2453      6.3751|
|  9:  3.2310 -  3.1067 1.00   1730  199 0.2239 0.2894      6.1792      6.2828|
| 10:  3.1067 -  2.9995 1.00   1727  189 0.2229 0.2688      6.0919      6.1941|
| 11:  2.9995 -  2.9058 1.00   1753  188 0.2310 0.2717       6.013      6.1527|
| 12:  2.9058 -  2.8227 1.00   1716  192 0.2237 0.2578      5.9517      6.0623|
| 13:  2.8227 -  2.7485 1.00   1705  185 0.2322 0.2941      5.8842      6.0254|
| 14:  2.7485 -  2.6814 1.00   1758  187 0.2346 0.2938      5.8513      5.9024|
| 15:  2.6814 -  2.6205 1.00   1681  216 0.2078 0.2762      5.7363      5.8757|
| 16:  2.6205 -  2.5647 1.00   1746  186 0.2133 0.2890      5.6817      5.8225|
| 17:  2.5647 -  2.5134 1.00   1748  174 0.2201 0.2889      5.6637      5.8262|
| 18:  2.5134 -  2.4660 1.00   1680  178 0.2190 0.2890      5.6254      5.6963|
| 19:  2.4660 -  2.4220 1.00   1745  202 0.2176 0.2987      5.5995      5.7843|
| 20:  2.4220 -  2.3809 1.00   1676  196 0.2202 0.2872      5.5916      5.7248|
| 21:  2.3809 -  2.3425 1.00   1731  207 0.2270 0.2920      5.5898      5.6889|
| 22:  2.3425 -  2.3065 1.00   1689  201 0.2375 0.3129      5.5909      5.7442|
| 23:  2.3065 -  2.2726 1.00   1711  193 0.2357 0.3093       5.564      5.6897|
| 24:  2.2726 -  2.2406 1.00   1703  165 0.2246 0.3157      5.5203      5.6882|
| 25:  2.2406 -  2.2103 1.00   1789  182 0.2201 0.2772        5.46      5.6264|
| 26:  2.2103 -  2.1816 1.00   1659  190 0.2225 0.3023      5.4435      5.5604|
| 27:  2.1816 -  2.1543 1.00   1728  202 0.2314 0.3067      5.4614      5.5789|
| 28:  2.1543 -  2.1284 1.00   1722  172 0.2478 0.3252      5.4451       5.573|
| 29:  2.1284 -  2.1036 1.00   1702  179 0.2237 0.3013      5.3531      5.5501|
| 30:  2.1036 -  2.0800 1.00   1732  200 0.2223 0.2851      5.3009      5.4312|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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  0.92  12.63   0.91     0.89      41473.94|
|  2:  6.4519 -  5.1255  1790   203  0.90  16.45   0.83     0.82      40593.06|
|  3:  5.1255 -  4.4788  1766   199  0.92  14.14   0.86     0.83      48499.44|
|  4:  4.4788 -  4.0699  1773   186  0.93  13.99   0.90     0.84      51986.60|
|  5:  4.0699 -  3.7785  1750   199  0.91  16.28   0.93     0.89      55753.10|
|  6:  3.7785 -  3.5559  1743   195  0.89  18.28   0.95     0.90      61261.61|
|  7:  3.5559 -  3.3779  1713   204  0.86  21.56   0.96     0.89      59091.80|
|  8:  3.3779 -  3.2310  1734   215  0.83  24.29   0.96     0.90      59446.48|
|  9:  3.2310 -  3.1067  1730   199  0.83  24.74   0.94     0.86      52204.62|
| 10:  3.1067 -  2.9995  1727   189  0.84  23.40   0.91     0.85      42219.07|
| 11:  2.9995 -  2.9058  1753   188  0.84  23.88   0.89     0.80      33486.54|
| 12:  2.9058 -  2.8227  1716   192  0.84  23.44   0.90     0.85      32404.16|
| 13:  2.8227 -  2.7485  1705   185  0.82  25.54   0.86     0.78      29554.33|
| 14:  2.7485 -  2.6814  1758   187  0.81  26.20   0.87     0.76      26374.02|
| 15:  2.6814 -  2.6205  1681   216  0.85  22.74   0.87     0.79      21438.69|
| 16:  2.6205 -  2.5647  1746   186  0.85  22.87   0.86     0.79      19303.08|
| 17:  2.5647 -  2.5134  1748   174  0.83  24.34   0.86     0.79      18911.27|
| 18:  2.5134 -  2.4660  1680   178  0.84  24.10   0.86     0.78      17775.27|
| 19:  2.4660 -  2.4220  1745   202  0.83  24.60   0.87     0.80      17497.72|
| 20:  2.4220 -  2.3809  1676   196  0.82  25.95   0.89     0.79      17314.34|
| 21:  2.3809 -  2.3425  1731   207  0.81  26.31   0.87     0.78      17117.39|
| 22:  2.3425 -  2.3065  1689   201  0.80  27.80   0.88     0.78      17562.34|
| 23:  2.3065 -  2.2726  1711   193  0.80  27.39   0.89     0.78      16675.46|
| 24:  2.2726 -  2.2406  1703   165  0.81  26.96   0.92     0.81      15650.55|
| 25:  2.2406 -  2.2103  1789   182  0.82  25.66   0.89     0.80      13181.03|
| 26:  2.2103 -  2.1816  1659   190  0.82  25.70   0.91     0.81      12567.06|
| 27:  2.1816 -  2.1543  1728   202  0.80  27.99   0.91     0.78      13568.26|
| 28:  2.1543 -  2.1284  1722   172  0.76  30.85   0.91     0.80      14303.90|
| 29:  2.1284 -  2.1036  1702   179  0.79  28.44   0.92     0.83      11963.39|
| 30:  2.1036 -  2.0800  1732   200  0.83  25.32   0.89     0.78       9238.75|
|alpha:            min =        0.75 max =            0.92 mean =         0.82|
|beta:             min =     8659.50 max =        62215.67 mean =     29751.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.92 mean =        23.33|
|phase err.(test): min =        0.00 max =           89.53 mean =        23.78|
|-----------------------------------------------------------------------------|

|-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:     5.162 -  11.527:  396   |   5:    36.990 -  43.355:  194        |
|      1:    11.527 -  17.893: 2360   |   6:    43.355 -  49.721:  116        |
|      2:    17.893 -  24.258: 2481   |   7:    49.721 -  56.086:   80        |
|      3:    24.258 -  30.624: 1105   |   8:    56.086 -  62.452:   54        |
|      4:    30.624 -  36.990:  501   |   9:    62.452 -  68.817:    7        |
|                               =>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)              
------------------------------------------------------------------------
 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    :  0.2588 0.2832   5.906458e+00   5.987779e+00
   1_bss:  0.2228 0.2556   5.873292e+00   5.957004e+00
   1_xyz:  0.2149 0.2580   5.853776e+00   5.961669e+00
   1_adp:  0.2087 0.2591   5.837085e+00   5.963333e+00
   2_bss:  0.2085 0.2587   5.837293e+00   5.963249e+00
   2_xyz:  0.2054 0.2596   5.831395e+00   5.966483e+00
   2_adp:  0.2054 0.2597   5.831102e+00   5.966952e+00
   3_bss:  0.2053 0.2595   5.832288e+00   5.967487e+00
   3_xyz:  0.2056 0.2601   5.833885e+00   5.969471e+00
   3_adp:  0.2058 0.2602   5.833195e+00   5.969120e+00
   3_bss:  0.2059 0.2590   5.832923e+00   5.967184e+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:  0.242  22.010  -1.127   0.927   1.371   0.000   0.000   0.000
   1_xyz:  0.242  22.010  -1.127   0.927   1.371   0.000   0.000   0.000
   1_adp:  0.242  22.010  -1.127   0.927   1.371   0.000   0.000   0.000
   2_bss:  0.245  20.001  -0.365   1.624   2.126   0.000   0.000   0.000
   2_xyz:  0.245  20.001  -0.365   1.624   2.126   0.000   0.000   0.000
   2_adp:  0.245  20.001  -0.365   1.624   2.126   0.000   0.000   0.000
   3_bss:  0.237  12.721   0.101   2.042   2.580   0.000   0.000   0.000
   3_xyz:  0.237  12.721   0.101   2.042   2.580   0.000   0.000   0.000
   3_adp:  0.237  12.721   0.101   2.042   2.580   0.000   0.000   0.000
   3_bss:  0.238  16.669  -1.462   0.460   1.001   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  24.063 0.8352  0.8028    34481.348
   1_bss:  23.174 0.8434  0.8234    28924.416
   1_xyz:  23.216 0.8432  0.8233    29481.906
   1_adp:  23.247 0.8429  0.8078    29608.685
   2_bss:  23.258 0.8427  0.8274    29568.599
   2_xyz:  23.326 0.8421  0.8272    29875.112
   2_adp:  23.333 0.8421  0.8111    29880.899
   3_bss:  23.385 0.8415  0.8199    29839.554
   3_xyz:  23.460 0.8407  0.8195    30020.058
   3_adp:  23.442 0.8409  0.8035    29999.041
   3_bss:  23.377 0.8415  0.8193    29780.662
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.107  0.006  0.083 19.352  0.006  4.114   7.6870e-02
   1_bss:   1.107  0.006  0.083 19.352  0.006  4.114   7.6870e-02
   1_xyz:   0.859  0.006  0.057 18.672  0.004  4.121   6.7518e-02
   1_adp:   0.859  0.006  0.057 18.672  0.004  4.121   6.7518e-02
   2_bss:   0.859  0.006  0.057 18.672  0.004  4.121   6.7518e-02
   2_xyz:   0.961  0.007  0.062 18.834  0.004  4.122   7.6134e-02
   2_adp:   0.961  0.007  0.062 18.834  0.004  4.122   7.6134e-02
   3_bss:   0.961  0.007  0.062 18.834  0.004  4.122   7.6134e-02
   3_xyz:   0.901  0.006  0.059 18.609  0.004  4.125   7.0898e-02
   3_adp:   0.901  0.006  0.059 18.609  0.004  4.125   7.0898e-02
   3_bss:   0.901  0.006  0.059 18.609  0.004  4.125   7.0898e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  12.824  0.053  0.310 89.106  0.044  2.397   4.3883e-02
   1_bss:  12.824  0.053  0.310 89.106  0.044  2.397   4.3883e-02
   1_xyz:   6.921  0.047  0.256 88.462  0.031  2.463   2.5038e-02
   1_adp:   6.921  0.047  0.256 88.462  0.031  2.463   2.5038e-02
   2_bss:   6.921  0.047  0.256 88.462  0.031  2.463   2.5038e-02
   2_xyz:   7.219  0.046  0.232 89.961  0.040  2.373   3.1526e-02
   2_adp:   7.219  0.046  0.232 89.961  0.040  2.373   3.1526e-02
   3_bss:   7.219  0.046  0.232 89.961  0.040  2.373   3.1526e-02
   3_xyz:   7.351  0.038  0.256 89.166  0.039  2.427   2.6037e-02
   3_adp:   7.351  0.038  0.256 89.166  0.039  2.427   2.6037e-02
   3_bss:   7.351  0.038  0.256 89.166  0.039  2.427   2.6037e-02
------------------------------------------------------------------------
 stage      b_max   b_min   b_ave
   0    :   55.11    6.00   21.13
   1_bss:   55.11    6.00   21.13
   1_xyz:   55.11    6.00   21.13
   1_adp:   66.55    3.45   20.78
   2_bss:   66.55    3.45   20.78
   2_xyz:   66.55    3.45   20.78
   2_adp:   66.57    3.13   20.21
   3_bss:   66.57    3.13   20.21
   3_xyz:   66.57    3.13   20.21
   3_adp:   66.69    3.03   19.66
   3_bss:   68.82    5.16   21.78
------------------------------------------------------------------------
 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:    0.430    0.002    0.068
   1_adp:    0.430    0.002    0.068
   2_bss:    0.430    0.002    0.068
   2_xyz:    0.593    0.003    0.089
   2_adp:    0.593    0.003    0.089
   3_bss:    0.593    0.003    0.089
   3_xyz:    0.798    0.004    0.100
   3_adp:    0.798    0.004    0.100
   3_bss:    0.798    0.004    0.100
------------------------------------------------------------------------

CPU time actual refinement: 402.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001.pdb
n_use            =  7294
n_use_u_iso      =  7294
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  7294
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

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 402.81 
  Macro-tasks:
    bulk solvent and scale       = 115.16 
    individual site refinement   = 186.51 
    weights calculation          = 44.59  
    collect and process          = 8.95   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 355.37 
  Micro-tasks:
    mask                            = 1.42   
    f_calc                          = 78.61  
    alpha_beta                      = 19.25  
    target                          = 2.12   
    gradients_wrt_atomic_parameters = 111.73 
    fmodel                         = 13.30  
    r_factors                      = 0.55   
    phase_errors                   = 19.82  
    foms                           = 0.43   
    TOTAL for micro-tasks          = 247.23 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.602 micro seconds
Total CPU time: 7.10 minutes
from_scatterers_fft:    213 calls, 77.82 s
gradients_fft:          189 calls, 91.91 s

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

# Date 2007-12-01 Time 00:54:39 PST -0800 (1196499279.32 s)
Start R-work = 0.2588, R-free = 0.2832 (no bulk solvent and anisotropic scale)
Final R-work = 0.2463, R-free = 0.2875 (no bulk solvent and anisotropic scale)

Start R-work = 0.2228, R-free = 0.2556
Final R-work = 0.2059, R-free = 0.2590