# Date 2008-05-28 Time 16:08:53 EDT -0400 (1212005333.71 s)
#phil __OFF__

Command line arguments: "nsf_d2_peak.sca" "1NSF.pdb" "refinement.input.xray_data.r_free_flags.generate=True"

HOST = cels023080
HOSTTYPE = x86_64-linux
USER = jbard
PID = 26799

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.3
  Release tag: rc2
  cctbx tag: 2008_05_25_1144
  Platform: intel-linux-2.6-x86_64 redhat-e5.1
  User: jbard
-------------------------------------------------------------------------------

              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.input.xray_data.r_free_flags.generate = True

Working crystal symmetry after inspecting all inputs:
  Unit cell: (115.986, 115.986, 44.151, 90, 90, 120)
  Space group: P 6 (No. 168)

  Monomer Library directory:
    "/d00/phenix/phenix-1.3-rc2/ext_ref_files/mon_lib"
  Total number of atoms: 2097
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: " "
      Number of atoms: 1943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1943
          Classifications: {'peptide': 247}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 233, 'PCIS': 1}
    Chain: " "
      Number of atoms: 154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 154
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2, 'water': 122}
          Link IDs: {None: 123}
  Time building chain proxies: 1.08, per 1000 atoms: 0.52


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

I-obs:
  nsf_d2_peak.sca:i_obs,sigma

Generating a new array of R-free flags.

Miller array info: nsf_d2_peak.sca:i_obs,sigma
Observation type: xray.intensity
Type of data: double, size=25420
Type of sigmas: double, size=25420
Number of Miller indices: 25420
Anomalous flag: True
Unit cell: (115.986, 115.986, 44.151, 90, 90, 120)
Space group: P 6 (No. 168)
Systematic absences: 0
Centric reflections: 995
Resolution range: 100.447 2.40028
Completeness in resolution range: 0.977429
Completeness with d_max=infinity: 0.977429
Bijvoet pairs: 12185
Lone Bijvoet mates: 55
Anomalous signal: 0.0902

Intensities converted to amplitudes for use in refinement.

Number of F-obs in resolution range:                   25420
Number of F-obs <= 0:                                  906
Refinement resolution range: d_max =  57.9930
                             d_min =   2.4003


Fobs statistics after all cutoffs applied:

Miller array info: None
Observation type: xray.amplitude
Type of data: double, size=24514
Type of sigmas: double, size=24514
Number of Miller indices: 24514
Anomalous flag: True
Unit cell: (115.986, 115.986, 44.151, 90, 90, 120)
Space group: P 6 (No. 168)
Systematic absences: 0
Centric reflections: 958
Resolution range: 57.993 2.40028
Completeness in resolution range: 0.942629
Completeness with d_max=infinity: 0.942592
Bijvoet pairs: 11440
Lone Bijvoet mates: 676
Anomalous signal: 0.0902
Miller array info: R-free-flags
Observation type: None
Type of data: bool, size=25420
Type of sigmas: None
Number of Miller indices: 25420
Anomalous flag: True
Unit cell: (115.986, 115.986, 44.151, 90, 90, 120)
Space group: P 6 (No. 168)
Systematic absences: 0
Centric reflections: 995
Resolution range: 100.447 2.40028
Completeness in resolution range: 0.977429
Completeness with d_max=infinity: 0.977429
Bijvoet pairs: 12185
Lone Bijvoet mates: 55

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 58.0099 -  5.1701 [2464/2607]  2216   248  10.1%
  bin  2:  5.1701 -  4.1040 [2535/2612]  2287   248   9.8%
  bin  3:  4.1040 -  3.5853 [2516/2602]  2255   261  10.4%
  bin  4:  3.5853 -  3.2576 [2518/2583]  2262   256  10.2%
  bin  5:  3.2576 -  3.0241 [2502/2591]  2258   244   9.8%
  bin  6:  3.0241 -  2.8458 [2519/2625]  2260   259  10.3%
  bin  7:  2.8458 -  2.7033 [2427/2557]  2174   253  10.4%
  bin  8:  2.7033 -  2.5856 [2437/2612]  2194   243  10.0%
  bin  9:  2.5856 -  2.4861 [2348/2605]  2129   219   9.3%
  bin 10:  2.4861 -  2.4003 [2248/2612]  2020   228  10.1%
                                overall 22055  2459  10.0%

No array of experimental phases found.

Writing MTZ file:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_data.mtz


========================== 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: 0.07 seconds
  Histogram of bond lengths:
        1.22 -     1.35: 631
        1.35 -     1.47: 412
        1.47 -     1.59: 944
        1.59 -     1.72: 5
        1.72 -     1.84: 16
  Bond restraints sorted by residual:
                 atom i - atom j                ideal  model  delta   weight residual
  pdb=" C5  ATP   858 " - pdb=" C4  ATP   858 " 1.490  1.382  0.108 2.50e+03 2.92e+01
  pdb=" SD  MET   657 " - pdb=" CE  MET   657 " 1.791  1.661  0.130 1.60e+03 2.70e+01
  pdb=" SD  MET   716 " - pdb=" CE  MET   716 " 1.791  1.690  0.101 1.60e+03 1.65e+01
  pdb=" SD  MET   655 " - pdb=" CE  MET   655 " 1.791  1.698  0.093 1.60e+03 1.37e+01
  pdb=" C5  ATP   858 " - pdb=" C6  ATP   858 " 1.490  1.425  0.065 2.50e+03 1.06e+01
  ... (remaining 2003 not shown)
  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 158
        2.72 -     3.27: 2455
        3.27 -     3.81: 3961
        3.81 -     4.36: 5350
        4.36 -     4.90: 7924
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb=" OG1 THR   550 " - pdb="MG    MG   859 "  2.176 3.250
  pdb=" O1B ATP   858 " - pdb="MG    MG   859 "  2.201 3.250
  pdb=" O1G ATP   858 " - pdb="MG    MG   859 "  2.201 3.250
  pdb="MG    MG   859 " - pdb=" O   HOH   767 "  2.271 3.250
  pdb="MG    MG   859 " - pdb=" O   HOH   765 "  2.301 3.250
  ... (remaining 19843 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.02: 686
       30.02 -    60.04: 67
       60.04 -    90.06: 17
       90.06 -   120.08: 2
      120.08 -   150.10: 2
  Dihedral angle restraints sorted by residual:
  pdb=" O2A ATP   858 "
  pdb=" PA  ATP   858 "
  pdb=" O5* ATP   858 "
  pdb=" C5* ATP   858 "
      ideal   model   delta periodicty    weight residual
      60.00 -149.90 -150.10     1       2.50e-03 5.63e+01
  pdb=" C2* ATP   858 "
  pdb=" C1* ATP   858 "
  pdb=" N9  ATP   858 "
  pdb=" C4  ATP   858 "
      ideal   model   delta periodicty    weight residual
      91.54  -52.11  143.65     1       2.50e-03 5.16e+01
  pdb=" PB  ATP   858 "
  pdb=" PA  ATP   858 "
  pdb=" O3A ATP   858 "
  pdb=" O2A ATP   858 "
      ideal   model   delta periodicty    weight residual
      59.99  -53.15  113.14     1       2.50e-03 3.20e+01
  ... (remaining 771 not shown)

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


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


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

Number of scattering types: 6
  Type Number    sf(0)   Gaussians
   S      11     15.96       2
   P       3     14.95       2
   Mg      1     11.95       2
   O     494      7.97       2
   N     331      6.97       2
   C    1257      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 =================

Refinement flags and selection counts:
  individual_sites       =  True (2097 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 2097 aniso = 0)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (0 atoms)
  group_anomalous        = False

n_use            =  2097
n_use_u_iso      =  2097
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 =  2097

==================== 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:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_001.eff

Writing geometry restraints to file:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_001.geo

CPU time processing inputs: 5.16


============================ 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 = 115.986 115.986 44.151 90 90 120
    space_group = "P 6"
  }
  input {
    pdb {
      file_name = "/dirs/home00/jbard/phenix/testxeon/1NSF.pdb"
    }
    xray_data {
      file_name = "nsf_d2_peak.sca"
      labels = "i_obs,sigma"
      r_free_flags {
        label = "R-free-flags"
        test_flag_value = 1
        generate = True
      }
    }
  }
  output {
    prefix = "1NSF_refine"
    serial = 1
  }
}
#phil __OFF__


=============================== refinement start ==============================


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


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

|--(resolution: 2.40 - 57.99 A; n_refl. = 24514)------------------------------|
|                                                                             |
| r_work= 0.3499   r_free= 0.3414   ksol= 0.00   Bsol= 0.00   scale= 0.109    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 3.802711                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 58.0099 -  6.2880 0.94   1224  138 0.5102 0.4202      5.1672      4.7634|
|  2:  6.2880 -  4.9918 0.96   1251  138 0.3008 0.3421      4.3272      4.3161|
|  3:  4.9918 -  4.3611 0.97   1270  139 0.2442 0.2717      4.3065      4.4505|
|  4:  4.3611 -  3.9624 0.96   1265  136 0.2336 0.2410      4.1886      4.2189|
|  5:  3.9624 -  3.6785 0.98   1254  148 0.2391 0.2369      4.1428      4.0682|
|  6:  3.6785 -  3.4616 0.97   1250  140 0.2518 0.2783      4.0249      4.1179|
|  7:  3.4616 -  3.2883 0.96   1267  146 0.2677 0.3000      3.8907      3.9482|
|  8:  3.2883 -  3.1452 0.98   1264  132 0.2962 0.3236       3.848      3.9629|
|  9:  3.1452 -  3.0241 0.96   1233  140 0.3186 0.2875      3.7748      3.7477|
| 10:  3.0241 -  2.9197 0.96   1252  142 0.3092 0.2998      3.6733      3.7373|
| 11:  2.9197 -  2.8284 0.96   1242  141 0.3278 0.2825      3.5833      3.6243|
| 12:  2.8284 -  2.7476 0.95   1202  139 0.3174 0.3328       3.475      3.5031|
| 13:  2.7476 -  2.6753 0.94   1253  150 0.3412 0.3360      3.4253      3.4832|
| 14:  2.6753 -  2.6100 0.94   1213  136 0.3460 0.3046      3.3416      3.3353|
| 15:  2.6100 -  2.5507 0.91   1211  113 0.3378 0.3893      3.3232      3.2557|
| 16:  2.5507 -  2.4964 0.89   1180  131 0.3580 0.3821      3.2404      3.2835|
| 17:  2.4964 -  2.4464 0.88   1093  126 0.3512 0.3565      3.2567      3.3369|
| 18:  2.4464 -  2.4003 0.86   1131  124 0.3560 0.2889      3.2801      3.1627|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 58.0099 -  6.2880  1224   138  0.59  44.80   0.06     0.07       2491.45|
|  2:  6.2880 -  4.9918  1251   138  0.65  40.25   0.12     0.11       1434.97|
|  3:  4.9918 -  4.3611  1270   139  0.84  23.46   0.14     0.13        784.63|
|  4:  4.3611 -  3.9624  1265   136  0.85  22.74   0.15     0.14        643.80|
|  5:  3.9624 -  3.6785  1254   148  0.84  22.86   0.15     0.14        500.39|
|  6:  3.6785 -  3.4616  1250   140  0.82  25.23   0.15     0.14        476.98|
|  7:  3.4616 -  3.2883  1267   146  0.80  27.74   0.14     0.14        410.42|
|  8:  3.2883 -  3.1452  1264   132  0.78  29.72   0.14     0.13        355.82|
|  9:  3.1452 -  3.0241  1233   140  0.77  29.74   0.14     0.13        274.76|
| 10:  3.0241 -  2.9197  1252   142  0.75  31.56   0.14     0.13        241.86|
| 11:  2.9197 -  2.8284  1242   141  0.74  33.07   0.13     0.13        200.71|
| 12:  2.8284 -  2.7476  1202   139  0.75  32.22   0.13     0.12        178.65|
| 13:  2.7476 -  2.6753  1253   150  0.72  34.86   0.13     0.12        154.89|
| 14:  2.6753 -  2.6100  1213   136  0.69  36.95   0.12     0.11        145.27|
| 15:  2.6100 -  2.5507  1211   113  0.70  35.99   0.13     0.11        132.22|
| 16:  2.5507 -  2.4964  1180   131  0.70  36.65   0.12     0.11        118.37|
| 17:  2.4964 -  2.4464  1093   126  0.72  34.78   0.13     0.12        101.03|
| 18:  2.4464 -  2.4003  1131   124  0.79  28.82   0.13     0.13         78.28|
|alpha:            min =        0.07 max =            0.14 mean =         0.12|
|beta:             min =       78.28 max =         2491.45 mean =       490.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.81 mean =        31.68|
|phase err.(test): min =        0.00 max =           88.53 mean =        31.97|
|-----------------------------------------------------------------------------|

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

Distribution of F-obs values before outliers rejection:
     0.447 - 28.837     : 13781
    28.837 - 57.227     : 6594
    57.227 - 85.617     : 2627
    85.617 - 114.006    : 1021
   114.006 - 142.396    : 349
   142.396 - 170.786    : 86
   170.786 - 199.176    : 39
   199.176 - 227.566    : 7
   227.566 - 255.955    : 7
   255.955 - 284.345    : 3

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 3
beamstop_shadow_outliers = 4
total                    = 7

Distribution of F-obs values after outliers rejection:
     0.447 - 28.837     : 13777
    28.837 - 57.227     : 6594
    57.227 - 85.617     : 2627
    85.617 - 114.006    : 1020
   114.006 - 142.396    : 349
   142.396 - 170.786    : 86
   170.786 - 199.176    : 38
   199.176 - 227.566    : 7
   227.566 - 255.955    : 6
   255.955 - 284.345    : 3

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.459101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.932   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.065340              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 92.738   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.013:  1893 |   0.000 -   1.424:  2312 |  2.176 -  2.448:        9 |
| 0.013 - 0.026:    84 |   1.424 -   2.848:   261 |  2.448 -  2.720:      149 |
| 0.026 - 0.039:    18 |   2.848 -   4.273:    78 |  2.720 -  2.993:     1158 |
| 0.039 - 0.052:     6 |   4.273 -   5.697:    33 |  2.993 -  3.265:     1297 |
| 0.052 - 0.065:     2 |   5.697 -   7.121:    19 |  3.265 -  3.538:     1547 |
| 0.065 - 0.078:     1 |   7.121 -   8.545:     8 |  3.538 -  3.810:     2414 |
| 0.078 - 0.091:     0 |   8.545 -   9.970:     3 |  3.810 -  4.083:     2422 |
| 0.091 - 0.104:     2 |   9.970 -  11.394:     3 |  4.083 -  4.355:     2928 |
| 0.104 - 0.117:     1 |  11.394 -  12.818:     0 |  4.355 -  4.628:     3758 |
| 0.117 - 0.130:     1 |  12.818 -  14.242:     1 |  4.628 -  4.900:     4166 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2008 |   0.009    0.130  0.000 |       0.139 |              |
|     angle |     2718 |   1.424   14.242  0.000 |       0.317 |              |
| chirality |      316 |   0.097    0.327  0.000 |       0.233 |        0.098 |
| planarity |      339 |   0.003    0.022  0.000 |       0.161 |              |
|  dihedral |      774 |  21.390  150.100  0.001 |       1.179 |              |
| nonbonded |     2008 |   4.106    4.900  2.176 |       0.181 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 33.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2097   0      16.83   74.15   35.46    None  None   None       |
|    all(noH): 2097   0      16.83   74.15   35.46    None  None   None       |
|    Sol.    : 122    0      22.12   65.41   42.70    None  None   None       |
|    Mac.    : 1975   0      16.83   74.15   35.01    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:    16.830 -  22.562:  138   |   5:    45.490 -  51.222:  221        |
|      1:    22.562 -  28.294:  445   |   6:    51.222 -  56.954:   99        |
|      2:    28.294 -  34.026:  506   |   7:    56.954 -  62.686:   52        |
|      3:    34.026 -  39.758:  386   |   8:    62.686 -  68.418:   14        |
|      4:    39.758 -  45.490:  232   |   9:    68.418 -  74.150:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.00   number of occupancies < 0.1 = 58     |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.3270   r_free= 0.3414   ksol= 0.00   Bsol= 0.00   scale= 0.118    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 3.792215                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.2178   r_free= 0.2230   ksol= 0.38   Bsol= 51.15   scale= 0.160   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,-3.42,27.89,-0.00,0.00,0.00); trace/3= 7.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 3.510071                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.300515              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.903   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.037842              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 95.752   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2178      final r-factor (work) = 0.1956          |
| start r-factor (free) = 0.2230      final r-factor (free) = 0.2297          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3733 = 3.30 * 0.50 * 3.8027 + 1.00 * 0.0978                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7171 = 3.30 * 0.50 * 3.4083 + 1.00 * 0.0925                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1956      final r-factor (work) = 0.1878          |
| start r-factor (free) = 0.2297      final r-factor (free) = 0.2337          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.1307 = 0.04 * 1.00 * 3.4083 + 1.00 * 0.0017                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.1295 = 0.04 * 1.00 * 3.3855 + 1.00 * 0.0014                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 33.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2097   0      15.89   87.72   35.93    None  None   None       |
|    all(noH): 2097   0      15.89   87.72   35.93    None  None   None       |
|    Sol.    : 122    0      18.74   57.09   39.43    None  None   None       |
|    Mac.    : 1975   0      15.89   87.72   35.71    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:    15.887 -  23.070:  149   |   5:    51.803 -  58.986:  120        |
|      1:    23.070 -  30.254:  569   |   6:    58.986 -  66.170:   55        |
|      2:    30.254 -  37.437:  622   |   7:    66.170 -  73.353:   17        |
|      3:    37.437 -  44.620:  346   |   8:    73.353 -  80.536:    5        |
|      4:    44.620 -  51.803:  212   |   9:    80.536 -  87.719:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1878   r_free= 0.2337   ksol= 0.38   Bsol= 51.15   scale= 0.162   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,-3.42,27.89,-0.00,0.00,0.00); trace/3= 7.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 3.393564                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1888   r_free= 0.2330   ksol= 0.38   Bsol= 51.15   scale= 0.162   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,-3.42,27.89,-0.00,0.00,0.00); trace/3= 7.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 3.397093                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.586349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.419  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.046105              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 172.128  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1888      final r-factor (work) = 0.1826          |
| start r-factor (free) = 0.2330      final r-factor (free) = 0.2344          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5590 = 5.59 * 0.50 * 3.3891 + 1.00 * 0.0926                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5299 = 5.59 * 0.50 * 3.3745 + 1.00 * 0.1043                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1826      final r-factor (work) = 0.1815          |
| start r-factor (free) = 0.2344      final r-factor (free) = 0.2354          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.1570 = 0.05 * 1.00 * 3.3745 + 1.00 * 0.0014                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.1570 = 0.05 * 1.00 * 3.3727 + 1.00 * 0.0015                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 33.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2097   0      15.12   88.21   35.90    None  None   None       |
|    all(noH): 2097   0      15.12   88.21   35.90    None  None   None       |
|    Sol.    : 122    0      18.69   55.98   39.02    None  None   None       |
|    Mac.    : 1975   0      15.12   88.21   35.70    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:    15.119 -  22.428:  123   |   5:    51.666 -  58.975:  117        |
|      1:    22.428 -  29.738:  555   |   6:    58.975 -  66.285:   59        |
|      2:    29.738 -  37.047:  636   |   7:    66.285 -  73.594:   17        |
|      3:    37.047 -  44.357:  357   |   8:    73.594 -  80.903:    5        |
|      4:    44.357 -  51.666:  226   |   9:    80.903 -  88.213:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1815   r_free= 0.2354   ksol= 0.38   Bsol= 51.15   scale= 0.162   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,-3.42,27.89,-0.00,0.00,0.00); trace/3= 7.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 3.374656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1815   r_free= 0.2358   ksol= 0.38   Bsol= 51.15   scale= 0.160   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.82,-3.82,26.63,-0.00,0.00,0.00); trace/3= 6.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 3.375669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.103271              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.591  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.043493              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 173.047  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1815      final r-factor (work) = 0.1827          |
| start r-factor (free) = 0.2358      final r-factor (free) = 0.2366          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0275 = 4.10 * 0.50 * 3.3744 + 1.00 * 0.1043                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0197 = 4.10 * 0.50 * 3.3789 + 1.00 * 0.0874                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1827      final r-factor (work) = 0.1831          |
| start r-factor (free) = 0.2366      final r-factor (free) = 0.2367          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.1485 = 0.04 * 1.00 * 3.3789 + 1.00 * 0.0015                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.1485 = 0.04 * 1.00 * 3.3805 + 1.00 * 0.0014                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 33.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2097   0      15.23   89.05   35.81    None  None   None       |
|    all(noH): 2097   0      15.23   89.05   35.81    None  None   None       |
|    Sol.    : 122    0      18.82   54.50   38.68    None  None   None       |
|    Mac.    : 1975   0      15.23   89.05   35.63    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:    15.227 -  22.610:  131   |   5:    52.140 -  59.522:  105        |
|      1:    22.610 -  29.992:  586   |   6:    59.522 -  66.905:   52        |
|      2:    29.992 -  37.375:  624   |   7:    66.905 -  74.287:   18        |
|      3:    37.375 -  44.757:  349   |   8:    74.287 -  81.670:    5        |
|      4:    44.757 -  52.140:  225   |   9:    81.670 -  89.052:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1831   r_free= 0.2367   ksol= 0.38   Bsol= 51.15   scale= 0.160   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.82,-3.82,26.63,-0.00,0.00,0.00); trace/3= 6.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 3.381025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 37.9701 -  6.2815 0.94   1220  138 0.1677 0.2044      4.0892      4.1467|
|  2:  6.2815 -  4.9894 0.96   1252  138 0.1925 0.2581      3.8967      4.0243|
|  3:  4.9894 -  4.3598 0.96   1278  139 0.1491 0.2062      3.9651      4.1219|
|  4:  4.3598 -  3.9616 0.97   1255  136 0.1443 0.1628      3.7795      3.8392|
|  5:  3.9616 -  3.6779 0.98   1253  148 0.1563 0.1980      3.7352      3.9115|
|  6:  3.6779 -  3.4612 0.97   1254  140 0.1661 0.2329      3.6956      3.9669|
|  7:  3.4612 -  3.2880 0.96   1263  146 0.1824 0.2422      3.6152      3.7454|
|  8:  3.2880 -  3.1449 0.98   1264  132 0.2009 0.2697       3.499      3.7404|
|  9:  3.1449 -  3.0239 0.96   1233  140 0.2050 0.2360       3.433      3.5748|
| 10:  3.0239 -  2.9196 0.96   1256  142 0.1945 0.2961      3.2947      3.7148|
| 11:  2.9196 -  2.8283 0.96   1238  141 0.2059 0.2287      3.1941      3.3661|
| 12:  2.8283 -  2.7475 0.95   1201  139 0.1967 0.2623      3.0749      3.2829|
| 13:  2.7475 -  2.6752 0.94   1253  150 0.2067 0.2513      3.0296      3.1916|
| 14:  2.6752 -  2.6100 0.94   1213  136 0.2227 0.2917      2.9698      3.2246|
| 15:  2.6100 -  2.5506 0.91   1211  113 0.1957 0.2955      2.8919      3.0004|
| 16:  2.5506 -  2.4964 0.89   1180  131 0.2185 0.3004        2.87      2.9881|
| 17:  2.4964 -  2.4464 0.88   1093  126 0.2146 0.2864      2.8495      3.1642|
| 18:  2.4464 -  2.4003 0.86   1131  124 0.2118 0.2427      2.7793      2.8898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 37.9701 -  6.2815  1220   138  0.88  18.31   0.16     0.15        537.35|
|  2:  6.2815 -  4.9894  1252   138  0.85  22.00   0.15     0.14        445.49|
|  3:  4.9894 -  4.3598  1278   139  0.91  15.40   0.17     0.18        427.39|
|  4:  4.3598 -  3.9616  1255   136  0.91  15.51   0.16     0.15        304.65|
|  5:  3.9616 -  3.6779  1253   148  0.89  17.66   0.17     0.16        311.88|
|  6:  3.6779 -  3.4612  1254   140  0.86  20.97   0.17     0.16        326.73|
|  7:  3.4612 -  3.2880  1263   146  0.84  23.80   0.17     0.16        296.95|
|  8:  3.2880 -  3.1449  1264   132  0.84  23.68   0.16     0.16        217.08|
|  9:  3.1449 -  3.0239  1233   140  0.81  26.33   0.16     0.15        206.48|
| 10:  3.0239 -  2.9196  1256   142  0.80  27.12   0.16     0.14        158.59|
| 11:  2.9196 -  2.8283  1238   141  0.77  30.09   0.15     0.15        144.34|
| 12:  2.8283 -  2.7475  1201   139  0.82  25.11   0.15     0.14         97.66|
| 13:  2.7475 -  2.6752  1253   150  0.78  28.88   0.15     0.14         99.18|
| 14:  2.6752 -  2.6100  1213   136  0.77  29.80   0.15     0.14         89.78|
| 15:  2.6100 -  2.5506  1211   113  0.79  28.26   0.15     0.13         76.50|
| 16:  2.5506 -  2.4964  1180   131  0.78  29.20   0.15     0.14         73.79|
| 17:  2.4964 -  2.4464  1093   126  0.79  27.88   0.16     0.14         60.43|
| 18:  2.4464 -  2.4003  1131   124  0.83  24.35   0.16     0.15         49.48|
|alpha:            min =        0.13 max =            0.18 mean =         0.15|
|beta:             min =       49.48 max =          537.35 mean =       221.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.78 mean =        24.06|
|phase err.(test): min =        0.00 max =           88.49 mean =        23.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1831   r_free= 0.2370   ksol= 0.38   Bsol= 61.68   scale= 0.160   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-10.08,-10.08,20.16,-0.00,0.00,0.00); trace/3= 0.00                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 3.380454                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.40 - 37.97 A; n_refl. = 24507)------------------------------|
|                                                                             |
| r_work= 0.1831   r_free= 0.2370   ksol= 0.38   Bsol= 61.68   scale= 0.160   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-10.08,-10.08,20.16,-0.00,0.00,0.00); trace/3= 0.00                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 3.380454                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 37.9701 -  6.2815 0.94   1220  138 0.1676 0.2064      4.0907      4.1523|
|  2:  6.2815 -  4.9894 0.96   1252  138 0.1935 0.2608      3.9017      4.0312|
|  3:  4.9894 -  4.3598 0.96   1278  139 0.1501 0.2088      3.9755       4.128|
|  4:  4.3598 -  3.9616 0.97   1255  136 0.1448 0.1643      3.7827      3.8457|
|  5:  3.9616 -  3.6779 0.98   1253  148 0.1567 0.1975      3.7379      3.9073|
|  6:  3.6779 -  3.4612 0.97   1254  140 0.1661 0.2332      3.6946      3.9713|
|  7:  3.4612 -  3.2880 0.96   1263  146 0.1818 0.2418      3.6141      3.7458|
|  8:  3.2880 -  3.1449 0.98   1264  132 0.2003 0.2700       3.497       3.741|
|  9:  3.1449 -  3.0239 0.96   1233  140 0.2043 0.2351      3.4304      3.5726|
| 10:  3.0239 -  2.9196 0.96   1256  142 0.1935 0.2945      3.2902      3.7095|
| 11:  2.9196 -  2.8283 0.96   1238  141 0.2053 0.2279      3.1906       3.362|
| 12:  2.8283 -  2.7475 0.95   1201  139 0.1959 0.2619      3.0714      3.2813|
| 13:  2.7475 -  2.6752 0.94   1253  150 0.2063 0.2501      3.0279      3.1898|
| 14:  2.6752 -  2.6100 0.94   1213  136 0.2218 0.2913      2.9665      3.2224|
| 15:  2.6100 -  2.5506 0.91   1211  113 0.1946 0.2951      2.8881      2.9984|
| 16:  2.5506 -  2.4964 0.89   1180  131 0.2176 0.2991      2.8672      2.9849|
| 17:  2.4964 -  2.4464 0.88   1093  126 0.2139 0.2847      2.8474      3.1607|
| 18:  2.4464 -  2.4003 0.86   1131  124 0.2108 0.2418      2.7771      2.8886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 37.9701 -  6.2815  1220   138  0.88  18.50   0.16     0.15        545.92|
|  2:  6.2815 -  4.9894  1252   138  0.85  22.18   0.15     0.14        452.05|
|  3:  4.9894 -  4.3598  1278   139  0.91  15.56   0.17     0.18        435.36|
|  4:  4.3598 -  3.9616  1255   136  0.91  15.55   0.16     0.15        305.91|
|  5:  3.9616 -  3.6779  1253   148  0.89  17.70   0.17     0.16        313.47|
|  6:  3.6779 -  3.4612  1254   140  0.86  20.94   0.17     0.16        325.42|
|  7:  3.4612 -  3.2880  1263   146  0.84  23.82   0.17     0.16        297.31|
|  8:  3.2880 -  3.1449  1264   132  0.84  23.65   0.16     0.16        216.58|
|  9:  3.1449 -  3.0239  1233   140  0.81  26.25   0.16     0.15        205.44|
| 10:  3.0239 -  2.9196  1256   142  0.80  26.94   0.16     0.14        156.99|
| 11:  2.9196 -  2.8283  1238   141  0.77  29.90   0.15     0.15        142.82|
| 12:  2.8283 -  2.7475  1201   139  0.82  24.98   0.15     0.14         96.76|
| 13:  2.7475 -  2.6752  1253   150  0.78  28.76   0.15     0.14         98.50|
| 14:  2.6752 -  2.6100  1213   136  0.77  29.67   0.15     0.14         89.11|
| 15:  2.6100 -  2.5506  1211   113  0.79  28.10   0.15     0.13         75.87|
| 16:  2.5506 -  2.4964  1180   131  0.78  29.03   0.15     0.14         73.10|
| 17:  2.4964 -  2.4464  1093   126  0.80  27.71   0.16     0.14         59.90|
| 18:  2.4464 -  2.4003  1131   124  0.83  24.23   0.16     0.15         49.17|
|alpha:            min =        0.13 max =            0.18 mean =         0.15|
|beta:             min =       49.17 max =          545.92 mean =       222.09|
|figures of merit: min =        0.01 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.52 mean =        24.01|
|phase err.(test): min =        0.00 max =           88.52 mean =        23.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 33.617)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2097   0      21.60   95.42   42.18    None  None   None       |
|    all(noH): 2097   0      21.60   95.42   42.18    None  None   None       |
|    Sol.    : 122    0      25.20   60.87   45.05    None  None   None       |
|    Mac.    : 1975   0      21.60   95.42   42.00    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:    21.599 -  28.981:  131   |   5:    58.511 -  65.894:  105        |
|      1:    28.981 -  36.364:  586   |   6:    65.894 -  73.276:   52        |
|      2:    36.364 -  43.746:  624   |   7:    73.276 -  80.659:   18        |
|      3:    43.746 -  51.129:  349   |   8:    80.659 -  88.041:    5        |
|      4:    51.129 -  58.511:  225   |   9:    88.041 -  95.424:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 88          
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 5.079
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 84 from: 88
   mapped sites are within: 0.867 - 5.079

peak=    4.300 closest distance to pdb=" N   LYS   489 " =    3.265
peak=    3.557 closest distance to pdb=" N   LYS   489 " =    5.079
peak=    3.731 closest distance to pdb=" N   LYS   489 " =    1.566
peak=    4.583 closest distance to pdb=" CB  LYS   489 " =    4.217
peak=    4.125 closest distance to pdb=" CB  ALA   491 " =    3.162
peak=    3.803 closest distance to pdb=" SD  MET   504 " =    2.403
peak=    5.944 closest distance to pdb=" O   ASN   505 " =    3.711
peak=    3.614 closest distance to pdb=" NE1 TRP   510 " =    1.679
peak=    5.104 closest distance to pdb=" NZ  LYS   529 " =    1.979
peak=    4.464 closest distance to pdb=" OE1 GLU   542 " =    2.525
peak=    4.151 closest distance to pdb=" NZ  LYS   555 " =    3.160
peak=    4.050 closest distance to pdb=" NZ  LYS   555 " =    1.807
peak=    3.781 closest distance to pdb=" NZ  LYS   555 " =    3.573
peak=    4.839 closest distance to pdb=" NZ  LYS   555 " =    1.962
peak=    4.574 closest distance to pdb=" NZ  LYS   555 " =    2.285
peak=    3.952 closest distance to pdb=" CG  PRO   570 " =    2.828
peak=    3.890 closest distance to pdb=" CG  PRO   570 " =    1.819
peak=    3.718 closest distance to pdb=" O   MET   573 " =    2.025
peak=    3.903 closest distance to pdb=" CA  ILE   574 " =    2.028
peak=    3.916 closest distance to pdb=" CG  GLN   583 " =    2.062
peak=    3.856 closest distance to pdb=" CE  LYS   586 " =    2.087
peak=    3.746 closest distance to pdb=" NZ  LYS   586 " =    3.133
peak=    4.023 closest distance to pdb=" OD2 ASP   590 " =    3.801
peak=    4.642 closest distance to pdb=" CB  GLN   596 " =    3.017
peak=    3.677 closest distance to pdb=" CD  ARG   607 " =    1.161
peak=    4.819 closest distance to pdb=" NE  ARG   607 " =    1.593
peak=    3.813 closest distance to pdb=" OH  TYR   611 " =    2.417
peak=    3.593 closest distance to pdb=" O   PRO   616 " =    3.833
peak=    6.840 closest distance to pdb=" CD  ARG   617 " =    2.515
peak=    4.192 closest distance to pdb=" NE  ARG   617 " =    4.012
peak=    4.127 closest distance to pdb=" CB  SER   619 " =    1.966
peak=    4.084 closest distance to pdb=" CB  LEU   626 " =    1.853
peak=    6.311 closest distance to pdb=" O   VAL   628 " =    2.717
peak=    5.803 closest distance to pdb=" SD  MET   655 " =    1.580
peak=    3.588 closest distance to pdb=" CB  MET   657 " =    1.729
peak=    4.388 closest distance to pdb=" O   LEU   658 " =    3.171
peak=    4.916 closest distance to pdb=" CE1 HIS   666 " =    3.887
peak=    4.001 closest distance to pdb=" CE1 HIS   666 " =    3.098
peak=    3.723 closest distance to pdb=" N   GLU   678 " =    1.695
peak=    4.665 closest distance to pdb=" N   PHE   686 " =    2.210
peak=    3.536 closest distance to pdb=" CE  LYS   687 " =    3.042
peak=    3.974 closest distance to pdb=" NZ  LYS   687 " =    2.675
peak=    4.280 closest distance to pdb=" OD1 ASP   688 " =    3.607
peak=    4.789 closest distance to pdb=" OD2 ASP   688 " =    2.339
peak=    3.641 closest distance to pdb=" N   LYS   689 " =    2.311
peak=    3.556 closest distance to pdb=" CG  LYS   701 " =    1.726
peak=    3.601 closest distance to pdb=" CD  LYS   701 " =    1.925
peak=    3.677 closest distance to pdb=" CE  LYS   702 " =    2.865
peak=    3.970 closest distance to pdb=" NZ  LYS   702 " =    2.782
peak=    5.262 closest distance to pdb=" O   TRP   704 " =    3.509
peak=    4.794 closest distance to pdb=" NE1 TRP   704 " =    1.767
peak=    4.319 closest distance to pdb=" CZ2 TRP   704 " =    4.141
peak=    5.636 closest distance to pdb=" CZ2 TRP   704 " =    4.709
peak=    4.420 closest distance to pdb=" CE  MET   712 " =    0.867
peak=    3.538 closest distance to pdb=" CE  MET   712 " =    1.151
peak=    3.875 closest distance to pdb=" O   LEU   718 " =    3.697
peak=    4.401 closest distance to pdb=" SD  MET   720 " =    1.426
peak=    3.623 closest distance to pdb=" CE  MET   720 " =    1.462
peak=    4.421 closest distance to pdb=" CB  PRO   722 " =    3.164
peak=    3.806 closest distance to pdb=" CD2 TYR   724 " =    3.549
peak=    4.614 closest distance to pdb=" CD  ARG   725 " =    1.989
peak=    3.550 closest distance to pdb=" N   LYS   728 " =    4.077
peak=    4.377 closest distance to pdb=" O   LEU   733 " =    3.618
peak=    5.116 closest distance to pdb=" O   LEU   733 " =    3.214
peak=    4.153 closest distance to pdb=" O   GLU   735 " =    3.684
peak=    4.356 closest distance to pdb=" O   GLU   735 " =    2.885
peak=    3.609 closest distance to pdb=" O   GLU   735 " =    2.068
peak=    4.922 closest distance to pdb=" O   HOH   736 " =    2.483
peak=    3.527 closest distance to pdb=" O   HOH   744 " =    1.921
peak=    4.323 closest distance to pdb=" O   HOH   744 " =    2.201
peak=    3.535 closest distance to pdb=" O   HOH   745 " =    2.795
peak=    3.896 closest distance to pdb=" O   HOH   757 " =    1.911
peak=    3.964 closest distance to pdb=" O   HOH   780 " =    2.686
peak=    4.103 closest distance to pdb=" O   HOH   790 " =    1.938
peak=    5.166 closest distance to pdb=" O   HOH   804 " =    3.457
peak=    4.247 closest distance to pdb=" O   HOH   804 " =    2.757
peak=    3.776 closest distance to pdb=" O   HOH   812 " =    2.140
peak=    4.027 closest distance to pdb=" O   HOH   817 " =    2.588
peak=    6.154 closest distance to pdb=" O   HOH   824 " =    2.627
peak=    4.993 closest distance to pdb=" O   HOH   829 " =    4.278
peak=    3.884 closest distance to pdb=" O   HOH   829 " =    2.893
peak=    4.308 closest distance to pdb=" O   HOH   843 " =    2.395
peak=    3.786 closest distance to pdb=" O   HOH   846 " =    2.223
peak=    4.517 closest distance to pdb=" O   HOH   846 " =    2.957

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 52          
Filter by distance & map next to the model:
   mapped sites are within: 0.042 - 4.358
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 35 from: 52
   mapped sites are within: 0.767 - 4.358

peak=   -3.986 closest distance to pdb=" NZ  LYS   509 " =    2.639
peak=   -3.935 closest distance to pdb=" CG  TRP   510 " =    1.195
peak=   -3.749 closest distance to pdb=" CG2 VAL   517 " =    2.718
peak=   -3.615 closest distance to pdb=" CG  ASP   519 " =    0.841
peak=   -4.280 closest distance to pdb=" CA  GLY   521 " =    2.648
peak=   -3.584 closest distance to pdb=" CG2 VAL   525 " =    2.777
peak=   -3.567 closest distance to pdb=" NH2 ARG   533 " =    4.358
peak=   -3.933 closest distance to pdb=" CG1 VAL   539 " =    2.673
peak=   -4.438 closest distance to pdb=" O   THR   550 " =    2.951
peak=   -3.717 closest distance to pdb=" CD1 ILE   556 " =    2.783
peak=   -3.823 closest distance to pdb=" CD1 ILE   556 " =    2.601
peak=   -3.556 closest distance to pdb=" CD1 ILE   556 " =    2.641
peak=   -3.965 closest distance to pdb=" CE1 PHE   576 " =    1.807
peak=   -3.635 closest distance to pdb=" O   CYS   582 " =    2.535
peak=   -3.676 closest distance to pdb=" CA  LYS   594 " =    2.060
peak=   -3.766 closest distance to pdb=" OD1 ASP   603 " =    2.687
peak=   -4.320 closest distance to pdb=" NH2 ARG   638 " =    2.849
peak=   -3.558 closest distance to pdb=" CD1 LEU   652 " =    2.387
peak=   -3.607 closest distance to pdb=" CE  MET   655 " =    1.117
peak=   -3.892 closest distance to pdb=" CE  MET   655 " =    2.047
peak=   -4.985 closest distance to pdb=" CZ  PHE   661 " =    2.659
peak=   -3.813 closest distance to pdb=" CG2 THR   663 " =    2.459
peak=   -5.957 closest distance to pdb=" CG2 THR   663 " =    2.767
peak=   -3.590 closest distance to pdb=" CD1 ILE   665 " =    2.363
peak=   -3.788 closest distance to pdb=" CG  PRO   668 " =    1.409
peak=   -3.803 closest distance to pdb=" CD  LYS   689 " =    2.257
peak=   -3.592 closest distance to pdb=" CE3 TRP   704 " =    1.681
peak=   -4.422 closest distance to pdb=" CD1 ILE   705 " =    3.096
peak=   -5.064 closest distance to pdb=" CD1 ILE   705 " =    2.758
peak=   -3.661 closest distance to pdb=" CD1 ILE   707 " =    2.072
peak=   -3.738 closest distance to pdb=" CE  LYS   709 " =    0.767
peak=   -3.797 closest distance to pdb=" CE2 TYR   724 " =    4.120
peak=   -4.099 closest distance to pdb=" O   LEU   733 " =    1.582
peak=   -4.140 closest distance to pdb=" C8  ATP   858 " =    2.752
peak=   -3.980 closest distance to pdb=" O   HOH   748 " =    2.380

================= 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_occ: refinement of occupancies                                        
------------------------------------------------------------------------
 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    :  0.3270 0.3414   3.792215e+00   3.807879e+00
   1_bss:  0.2178 0.2230   3.510071e+00   3.511501e+00
   1_xyz:  0.1956 0.2297   3.419232e+00   3.533438e+00
   1_adp:  0.1878 0.2337   3.393564e+00   3.548106e+00
   2_bss:  0.1888 0.2330   3.397093e+00   3.547225e+00
   2_xyz:  0.1826 0.2344   3.377542e+00   3.554923e+00
   2_adp:  0.1815 0.2354   3.374656e+00   3.559118e+00
   3_bss:  0.1815 0.2358   3.375669e+00   3.560600e+00
   3_xyz:  0.1827 0.2366   3.379308e+00   3.562461e+00
   3_adp:  0.1831 0.2367   3.381025e+00   3.562911e+00
   3_bss:  0.1831 0.2370   3.380454e+00   3.562880e+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:  0.383  51.153  -3.424  -3.424  27.885  -0.000   0.000   0.000
   1_xyz:  0.383  51.153  -3.424  -3.424  27.885  -0.000   0.000   0.000
   1_adp:  0.383  51.153  -3.424  -3.424  27.885  -0.000   0.000   0.000
   2_bss:  0.383  51.153  -3.424  -3.424  27.885  -0.000   0.000   0.000
   2_xyz:  0.383  51.153  -3.424  -3.424  27.885  -0.000   0.000   0.000
   2_adp:  0.383  51.153  -3.424  -3.424  27.885  -0.000   0.000   0.000
   3_bss:  0.382  51.153  -3.825  -3.825  26.627  -0.000   0.000   0.000
   3_xyz:  0.382  51.153  -3.825  -3.825  26.627  -0.000   0.000   0.000
   3_adp:  0.382  51.153  -3.825  -3.825  26.627  -0.000   0.000   0.000
   3_bss:  0.380  61.685 -10.078 -10.078  20.155  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.703 0.7498  0.1232      490.585
   1_bss:  22.409 0.8480  0.1540      201.571
   1_xyz:  23.011 0.8416  0.1537      208.780
   1_adp:  23.735 0.8337  0.1535      216.102
   2_bss:  23.718 0.8338  0.1536      213.509
   2_xyz:  23.881 0.8320  0.1533      217.762
   2_adp:  24.036 0.8303  0.1527      219.571
   3_bss:  23.988 0.8310  0.1505      220.031
   3_xyz:  24.029 0.8306  0.1504      220.897
   3_adp:  24.042 0.8304  0.1501      221.215
   3_bss:  23.997 0.8310  0.1504      222.131
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.424  0.009  0.097 21.390  0.003  4.106   9.7825e-02
   1_bss:   1.424  0.009  0.097 21.390  0.003  4.106   9.7825e-02
   1_xyz:   1.161  0.008  0.068 20.641  0.006  4.113   9.2490e-02
   1_adp:   1.161  0.008  0.068 20.641  0.006  4.113   9.2490e-02
   2_bss:   1.161  0.008  0.068 20.641  0.006  4.113   9.2490e-02
   2_xyz:   1.243  0.009  0.071 21.002  0.007  4.112   1.0433e-01
   2_adp:   1.243  0.009  0.071 21.002  0.007  4.112   1.0433e-01
   3_bss:   1.243  0.009  0.071 21.002  0.007  4.112   1.0433e-01
   3_xyz:   1.088  0.007  0.063 20.483  0.006  4.113   8.7443e-02
   3_adp:   1.088  0.007  0.063 20.483  0.006  4.113   8.7443e-02
   3_bss:   1.088  0.007  0.063 20.483  0.006  4.113   8.7443e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  14.242  0.130  0.327150.100  0.022  2.176   1.0904e-01
   1_bss:  14.242  0.130  0.327150.100  0.022  2.176   1.0904e-01
   1_xyz:  10.056  0.048  0.292138.132  0.051  2.132   6.8059e-02
   1_adp:  10.056  0.048  0.292138.132  0.051  2.132   6.8059e-02
   2_bss:  10.056  0.048  0.292138.132  0.051  2.132   6.8059e-02
   2_xyz:  10.519  0.055  0.319138.678  0.055  2.114   7.1279e-02
   2_adp:  10.519  0.055  0.319138.678  0.055  2.114   7.1279e-02
   3_bss:  10.519  0.055  0.319138.678  0.055  2.114   7.1279e-02
   3_xyz:   9.804  0.045  0.293138.499  0.055  2.149   5.2042e-02
   3_adp:   9.804  0.045  0.293138.499  0.055  2.149   5.2042e-02
   3_bss:   9.804  0.045  0.293138.499  0.055  2.149   5.2042e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  74.15  16.83  35.46  74.15  16.83  35.01  65.41  22.12  42.70
   1_bss:  74.15  16.83  35.46  74.15  16.83  35.01  65.41  22.12  42.70
   1_xyz:  74.15  16.83  35.46  74.15  16.83  35.01  65.41  22.12  42.70
   1_adp:  87.72  15.89  35.93  87.72  15.89  35.71  57.09  18.74  39.43
   2_bss:  87.72  15.89  35.93  87.72  15.89  35.71  57.09  18.74  39.43
   2_xyz:  87.72  15.89  35.93  87.72  15.89  35.71  57.09  18.74  39.43
   2_adp:  88.21  15.12  35.90  88.21  15.12  35.70  55.98  18.69  39.02
   3_bss:  88.21  15.12  35.90  88.21  15.12  35.70  55.98  18.69  39.02
   3_xyz:  88.21  15.12  35.90  88.21  15.12  35.70  55.98  18.69  39.02
   3_adp:  89.05  15.23  35.81  89.05  15.23  35.63  54.50  18.82  38.68
   3_bss:  95.42  21.60  42.18  95.42  21.60  42.00  60.87  25.20  45.05
------------------------------------------------------------------------
 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:    0.633    0.005    0.124
   1_adp:    0.633    0.005    0.124
   2_bss:    0.633    0.005    0.124
   2_xyz:    1.013    0.005    0.159
   2_adp:    1.013    0.005    0.159
   3_bss:    1.013    0.005    0.159
   3_xyz:    1.120    0.006    0.165
   3_adp:    1.120    0.006    0.165
   3_bss:    1.120    0.006    0.165
------------------------------------------------------------------------

CPU time actual refinement: 138.79


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

Writing refined structure to PDB file:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_001.pdb
n_use            =  2097
n_use_u_iso      =  2097
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  2097
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 =  2097

Writing 2mFo-DFc XPLOR map to file:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_001_2mFo-DFc.map
Writing mFo-DFc XPLOR map to file:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_001_mFo-DFc.map
Writing map coefficients to MTZ file:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /dirs/home00/jbard/phenix/testxeon/1NSF_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 138.69 
  Macro-tasks:
    bulk solvent and scale       = 25.49  
    individual site refinement   = 74.84  
    weights calculation          = 14.12  
    collect and process          = 3.83   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 118.41 
  Micro-tasks:
    mask                            = 0.42   
    f_calc                          = 32.60  
    alpha_beta                      = 7.07   
    target                          = 0.68   
    gradients_wrt_atomic_parameters = 46.05  
    fmodel                         = 3.93   
    r_factors                      = 0.19   
    phase_errors                   = 8.27   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 99.43  
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 3.215 micro seconds
Total CPU time: 2.46 minutes
from_scatterers_fft:    230 calls, 32.46 s
gradients_fft:          195 calls, 43.06 s

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

# Date 2008-05-28 Time 16:11:22 EDT -0400 (1212005482.16 s)
Start R-work = 0.3270, R-free = 0.3414 (no bulk solvent and anisotropic scale)
Final R-work = 0.3328, R-free = 0.3667 (no bulk solvent and anisotropic scale)

Start R-work = 0.2178, R-free = 0.2230
Final R-work = 0.1831, R-free = 0.2370