# Date 2008-01-16 Time 03:23:04 PST -0800 (1200482584.14 s)
#phil __OFF__

Command line arguments: "../1217.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10812
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1217

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 45.7567, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.95474
Completeness in resolution range: 0.912304
Completeness with d_max=infinity: 0.909762

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   1.9547

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.95474
Completeness in resolution range: 0.912304
Completeness with d_max=infinity: 0.909762

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.1854 [2251/2278]  2027   224  10.0%
  bin  2:  4.1854 -  3.3333 [2171/2191]  1956   215   9.9%
  bin  3:  3.3333 -  2.9153 [2137/2156]  1916   221  10.3%
  bin  4:  2.9153 -  2.6502 [2099/2129]  1889   210  10.0%
  bin  5:  2.6502 -  2.4611 [2129/2148]  1918   211   9.9%
  bin  6:  2.4611 -  2.3165 [2097/2122]  1884   213  10.2%
  bin  7:  2.3165 -  2.2009 [2086/2114]  1874   212  10.2%
  bin  8:  2.2009 -  2.1053 [2078/2114]  1879   199   9.6%
  bin  9:  2.1053 -  2.0245 [1967/2108]  1776   191   9.7%
  bin 10:  2.0245 -  1.9547 [ 574/2112]   511    63  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_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=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.57 -     2.24: 24
        2.24 -     2.90: 1403
        2.90 -     3.57: 4502
        3.57 -     4.23: 9177
        4.23 -     4.90: 13128
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.570 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28229 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 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      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


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

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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 = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
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 =  2823

==================== 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/tmp/phzwart/tassos/trial/run_1217/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_refine_001.geo

CPU time processing inputs: 7.97


============================ 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 = 72.00625 45.75675 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5204   r_free= 0.5127   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.317647                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6694 0.99   1465  164 0.4502 0.4504      6.6865      6.7138|
|  2:  4.6694 -  3.7238 0.99   1412  154 0.4694 0.4511      6.8948      6.8839|
|  3:  3.7238 -  3.2583 0.99   1375  152 0.4987 0.4792      6.7128      6.6988|
|  4:  3.2583 -  2.9627 0.99   1370  159 0.5146 0.5323      6.5582      6.5468|
|  5:  2.9627 -  2.7517 0.99   1371  151 0.5502 0.5199      6.3884      6.3927|
|  6:  2.7517 -  2.5903 0.99   1344  149 0.5455 0.5302      6.2949      6.2376|
|  7:  2.5903 -  2.4611 0.99   1369  152 0.5661 0.5099      6.2416      6.1576|
|  8:  2.4611 -  2.3544 0.98   1339  147 0.5493 0.5614      6.1761      6.2299|
|  9:  2.3544 -  2.2640 0.98   1332  153 0.5490 0.5416      6.1424      6.1743|
| 10:  2.2640 -  2.1861 1.00   1346  150 0.5445 0.5345      6.0741      6.0451|
| 11:  2.1861 -  2.1180 0.98   1335  148 0.5307 0.5695      6.0242      6.0638|
| 12:  2.1180 -  2.0576 0.98   1341  141 0.5519 0.5608      5.9365      5.9045|
| 13:  2.0576 -  2.0035 0.75    998  118 0.5680 0.4895      5.8828      5.8033|
| 14:  2.0035 -  1.9547 0.17    233   21 0.5740 0.4782      5.8765      5.9531|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.6694  1465   164  0.62  41.22   0.76     0.69     101438.50|
|  2:  4.6694 -  3.7238  1412   154  0.61  43.22   0.82     0.69     150217.28|
|  3:  3.7238 -  3.2583  1375   152  0.44  56.38   0.81     0.58     160123.36|
|  4:  3.2583 -  2.9627  1370   159  0.32  65.78   0.73     0.42     143395.43|
|  5:  2.9627 -  2.7517  1371   151  0.23  72.92   0.70     0.30     108963.85|
|  6:  2.7517 -  2.5903  1344   149  0.22  73.55   0.69     0.27      90237.63|
|  7:  2.5903 -  2.4611  1369   152  0.20  74.90   0.71     0.25      76257.19|
|  8:  2.4611 -  2.3544  1339   147  0.19  76.01   0.70     0.23      69934.75|
|  9:  2.3544 -  2.2640  1332   153  0.16  77.80   0.72     0.20      65200.70|
| 10:  2.2640 -  2.1861  1346   150  0.16  77.83   0.72     0.21      58602.38|
| 11:  2.1861 -  2.1180  1335   148  0.18  76.33   0.75     0.24      55519.20|
| 12:  2.1180 -  2.0576  1341   141  0.19  75.61   0.71     0.26      48373.13|
| 13:  2.0576 -  2.0035   998   118  0.21  74.33   0.69     0.29      41884.00|
| 14:  2.0035 -  1.9547   233    21  0.28  69.32   0.74     0.33      32208.48|
|alpha:            min =        0.20 max =            0.69 mean =         0.36|
|beta:             min =    32208.48 max =       160123.36 mean =     90757.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.29|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.74|
|phase err.(test): min =        0.00 max =           89.97 mean =        67.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 30.381569             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.479   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.576776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.200   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      707 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1499 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2640 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3924 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5068 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6528 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7688 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.844 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.271 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5223   r_free= 0.5127   ksol= 0.00   Bsol= 0.00   scale= 0.731    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.318278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5125   r_free= 0.5028   ksol= 0.34   Bsol= 20.00   scale= 0.934   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.20,7.85,7.49,0.00,0.00,0.00); trace/3= 7.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.315748                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 24.789156             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.207   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.537350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.214   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5125      final r-factor (work) = 0.4616          |
| start r-factor (free) = 0.5028      final r-factor (free) = 0.4816          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 132.0711 = 24.79 * 0.50 * 6.3114 + 1.00 * 53.8437                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.9822 = 24.79 * 0.50 * 6.2788 + 1.00 * 0.1597                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4616      final r-factor (work) = 0.4259          |
| start r-factor (free) = 0.4816      final r-factor (free) = 0.4899          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9458 = 2.54 * 1.00 * 6.2788 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.8642 = 2.54 * 1.00 * 6.2423 + 1.00 * 0.0254                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.25   18.20    None  None   None       |
|    all(noH): 2823   0      0.00    88.25   18.20    None  None   None       |
|    Sol.    : 438    0      0.00    88.04   24.97    None  None   None       |
|    Mac.    : 2385   0      0.00    88.25   16.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.825:  807   |   5:    44.126 -  52.952:   93        |
|      1:     8.825 -  17.651:  800   |   6:    52.952 -  61.777:   42        |
|      2:    17.651 -  26.476:  585   |   7:    61.777 -  70.602:   20        |
|      3:    26.476 -  35.301:  302   |   8:    70.602 -  79.427:    7        |
|      4:    35.301 -  44.126:  160   |   9:    79.427 -  88.253:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4259 r_free = 0.4899             target_work(ml) = 6.243         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4254 r_free = 0.4892             target_work(ml) = 6.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4254   r_free= 0.4892   ksol= 0.34   Bsol= 20.00   scale= 1.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.20,7.85,7.49,0.00,0.00,0.00); trace/3= 7.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.242058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4238   r_free= 0.4883   ksol= 0.35   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,3.87,3.80,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.242877                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.023913             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.961  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.940354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.497  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4238      final r-factor (work) = 0.3842          |
| start r-factor (free) = 0.4883      final r-factor (free) = 0.4716          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.0285 = 15.02 * 0.50 * 6.2392 + 1.00 * 0.1597                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.7388 = 15.02 * 0.50 * 6.2093 + 1.00 * 0.0946                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3842      final r-factor (work) = 0.3811          |
| start r-factor (free) = 0.4716      final r-factor (free) = 0.4600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8643 = 0.94 * 1.00 * 6.2093 + 1.00 * 0.0253                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8276 = 0.94 * 1.00 * 6.1858 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.16   16.31    None  None   None       |
|    all(noH): 2823   0      0.00    80.16   16.31    None  None   None       |
|    Sol.    : 438    0      0.00    80.16   23.35    None  None   None       |
|    Mac.    : 2385   0      0.00    65.34   15.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.016:  700   |   5:    40.079 -  48.094:   74        |
|      1:     8.016 -  16.031:  929   |   6:    48.094 -  56.110:   30        |
|      2:    16.031 -  24.047:  606   |   7:    56.110 -  64.126:   11        |
|      3:    24.047 -  32.063:  328   |   8:    64.126 -  72.141:    3        |
|      4:    32.063 -  40.079:  138   |   9:    72.141 -  80.157:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3811 r_free = 0.4600             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3810 r_free = 0.4595             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3810   r_free= 0.4595   ksol= 0.35   Bsol= 50.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,3.87,3.80,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.174741                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3816   r_free= 0.4595   ksol= 0.34   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,2.37,3.12,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.176240                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.320958             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.839  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.835866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.097  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3816      final r-factor (work) = 0.3293          |
| start r-factor (free) = 0.4595      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2044 = 12.32 * 0.50 * 6.1862 + 1.00 * 0.0946                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.8792 = 12.32 * 0.50 * 6.1321 + 1.00 * 0.1027                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3293      final r-factor (work) = 0.3086          |
| start r-factor (free) = 0.4083      final r-factor (free) = 0.3996          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1364 = 0.84 * 1.00 * 6.1321 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0652 = 0.84 * 1.00 * 6.0437 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.88   16.79    None  None   None       |
|    all(noH): 2823   0      0.00    76.88   16.79    None  None   None       |
|    Sol.    : 438    0      0.00    73.65   29.62    None  None   None       |
|    Mac.    : 2385   0      0.00    76.88   14.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.688:  731   |   5:    38.441 -  46.129:  101        |
|      1:     7.688 -  15.377:  823   |   6:    46.129 -  53.818:   52        |
|      2:    15.377 -  23.065:  568   |   7:    53.818 -  61.506:   24        |
|      3:    23.065 -  30.753:  334   |   8:    61.506 -  69.194:   11        |
|      4:    30.753 -  38.441:  174   |   9:    69.194 -  76.882:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3086 r_free = 0.3996             target_work(ml) = 6.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3083 r_free = 0.3993             target_work(ml) = 6.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3083   r_free= 0.3993   ksol= 0.34   Bsol= 50.00   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,2.37,3.12,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.029835                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3081   r_free= 0.3985   ksol= 0.35   Bsol= 72.10   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,0.98,2.11,0.00,0.00,0.00); trace/3= 1.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.028996                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.621736             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.681   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.118156              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.869  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2475          |
| start r-factor (free) = 0.3985      final r-factor (free) = 0.3285          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2199 = 11.62 * 0.50 * 6.0433 + 1.00 * 0.1030                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7164 = 11.62 * 0.50 * 5.9543 + 1.00 * 0.1170                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2475      final r-factor (work) = 0.2191          |
| start r-factor (free) = 0.3285      final r-factor (free) = 0.2979          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6711 = 1.12 * 1.00 * 5.9543 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5105 = 1.12 * 1.00 * 5.8024 + 1.00 * 0.0226                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.35   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    88.35   17.30    None  None   None       |
|    Sol.    : 438    0      0.00    85.37   41.37    None  None   None       |
|    Mac.    : 2385   0      0.00    88.35   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.835: 1059   |   5:    44.173 -  53.008:  106        |
|      1:     8.835 -  17.669:  836   |   6:    53.008 -  61.842:   89        |
|      2:    17.669 -  26.504:  360   |   7:    61.842 -  70.677:   45        |
|      3:    26.504 -  35.338:  185   |   8:    70.677 -  79.511:   14        |
|      4:    35.338 -  44.173:  123   |   9:    79.511 -  88.346:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2191 r_free = 0.2979             target_work(ml) = 5.750         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2189 r_free = 0.2977             target_work(ml) = 5.749         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2189   r_free= 0.2977   ksol= 0.35   Bsol= 72.10   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,0.98,2.11,0.00,0.00,0.00); trace/3= 1.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.748782                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2187   r_free= 0.2972   ksol= 0.34   Bsol= 72.10   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.85,-0.03,1.57,-0.00,0.00,0.00); trace/3= 0.80                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.747316                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.589778              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.335   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.203   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2187      final r-factor (work) = 0.1775          |
| start r-factor (free) = 0.2972      final r-factor (free) = 0.2446          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2362 = 6.59 * 0.50 * 5.8027 + 1.00 * 0.1170                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7707 = 6.59 * 0.50 * 5.6725 + 1.00 * 0.0803                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1775      final r-factor (work) = 0.1672          |
| start r-factor (free) = 0.2446      final r-factor (free) = 0.2251          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1878 = 0.21 * 1.00 * 5.6725 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1532 = 0.21 * 1.00 * 5.5500 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    84.83   15.92    None  None   None       |
|    all(noH): 2823   0      0.99    84.83   15.92    None  None   None       |
|    Sol.    : 438    0      3.91    74.77   39.56    None  None   None       |
|    Mac.    : 2385   0      0.99    84.83   11.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.991 -   9.375: 1228   |   5:    42.911 -  51.295:   87        |
|      1:     9.375 -  17.759:  861   |   6:    51.295 -  59.679:   89        |
|      2:    17.759 -  26.143:  250   |   7:    59.679 -  68.063:   37        |
|      3:    26.143 -  34.527:  140   |   8:    68.063 -  76.447:   12        |
|      4:    34.527 -  42.911:  118   |   9:    76.447 -  84.831:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1672 r_free = 0.2251             target_work(ml) = 5.499         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1669 r_free = 0.2244             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1669   r_free= 0.2244   ksol= 0.34   Bsol= 72.10   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.85,-0.03,1.57,-0.00,0.00,0.00); trace/3= 0.80                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.497461                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6694 0.99   1465  164 0.1119 0.1633       5.525      5.7955|
|  2:  4.6694 -  3.7238 0.99   1412  154 0.1145 0.1596      5.7233       6.031|
|  3:  3.7238 -  3.2583 0.99   1375  152 0.1597 0.2194      5.8116      6.0474|
|  4:  3.2583 -  2.9627 0.99   1370  159 0.1893 0.2377      5.7913      5.9554|
|  5:  2.9627 -  2.7517 0.99   1371  151 0.1943 0.2609      5.6752      5.8882|
|  6:  2.7517 -  2.5903 0.99   1344  149 0.1901 0.2772      5.5741       5.766|
|  7:  2.5903 -  2.4611 0.99   1369  152 0.1923 0.2430      5.4992      5.6652|
|  8:  2.4611 -  2.3544 0.98   1339  147 0.1929 0.2337      5.4507       5.632|
|  9:  2.3544 -  2.2640 0.98   1332  153 0.1806 0.2517      5.3738      5.6008|
| 10:  2.2640 -  2.1861 1.00   1346  150 0.1779 0.2389      5.3107       5.492|
| 11:  2.1861 -  2.1180 0.98   1335  148 0.1745 0.2508      5.2699      5.6185|
| 12:  2.1180 -  2.0576 0.98   1341  141 0.1870 0.2684      5.2503      5.4638|
| 13:  2.0576 -  2.0035 0.75    998  118 0.1967 0.2307      5.1742      5.2986|
| 14:  2.0035 -  1.9547 0.17    233   21 0.1630 0.2317      5.0409       5.289|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.6694  1465   164  0.92  12.19   0.97     0.95      10916.30|
|  2:  4.6694 -  3.7238  1412   154  0.92  12.30   1.03     1.03      16403.43|
|  3:  3.7238 -  3.2583  1375   152  0.87  18.59   1.05     1.05      21072.43|
|  4:  3.2583 -  2.9627  1370   159  0.84  22.22   1.03     1.00      21088.99|
|  5:  2.9627 -  2.7517  1371   151  0.82  24.26   1.03     0.99      18046.18|
|  6:  2.7517 -  2.5903  1344   149  0.80  26.17   1.01     0.93      15484.82|
|  7:  2.5903 -  2.4611  1369   152  0.82  24.27   1.02     0.97      12771.43|
|  8:  2.4611 -  2.3544  1339   147  0.81  25.16   1.01     0.94      11748.55|
|  9:  2.3544 -  2.2640  1332   153  0.83  24.06   1.03     0.96      10154.14|
| 10:  2.2640 -  2.1861  1346   150  0.82  24.49   1.04     0.98       9189.80|
| 11:  2.1861 -  2.1180  1335   148  0.82  24.28   1.05     0.98       8817.32|
| 12:  2.1180 -  2.0576  1341   141  0.80  26.32   1.03     1.02       8850.35|
| 13:  2.0576 -  2.0035   998   118  0.81  26.26   1.02     0.96       7072.17|
| 14:  2.0035 -  1.9547   233    21  0.86  21.15   1.04     1.00       5146.24|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     5146.24 max =        21088.99 mean =     13249.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.98 mean =        22.15|
|phase err.(test): min =        0.00 max =           89.94 mean =        20.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1668   r_free= 0.2233   ksol= 0.33   Bsol= 55.58   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.01,-0.94,0.93,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.495653                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1668   r_free= 0.2233   ksol= 0.33   Bsol= 55.58   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.01,-0.94,0.93,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.495653                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6694 0.99   1465  164 0.1125 0.1582      5.5121       5.763|
|  2:  4.6694 -  3.7238 0.99   1412  154 0.1143 0.1548      5.7133      6.0115|
|  3:  3.7238 -  3.2583 0.99   1375  152 0.1596 0.2185      5.8063      6.0429|
|  4:  3.2583 -  2.9627 0.99   1370  159 0.1898 0.2372        5.79      5.9509|
|  5:  2.9627 -  2.7517 0.99   1371  151 0.1949 0.2621      5.6758      5.8912|
|  6:  2.7517 -  2.5903 0.99   1344  149 0.1902 0.2776      5.5747      5.7658|
|  7:  2.5903 -  2.4611 0.99   1369  152 0.1926 0.2435      5.5006      5.6659|
|  8:  2.4611 -  2.3544 0.98   1339  147 0.1931 0.2350      5.4517      5.6337|
|  9:  2.3544 -  2.2640 0.98   1332  153 0.1807 0.2514      5.3744      5.5983|
| 10:  2.2640 -  2.1861 1.00   1346  150 0.1780 0.2401      5.3116      5.4949|
| 11:  2.1861 -  2.1180 0.98   1335  148 0.1744 0.2515      5.2701      5.6195|
| 12:  2.1180 -  2.0576 0.98   1341  141 0.1870 0.2695      5.2523      5.4673|
| 13:  2.0576 -  2.0035 0.75    998  118 0.1969 0.2299      5.1745      5.2975|
| 14:  2.0035 -  1.9547 0.17    233   21 0.1632 0.2325      5.0408      5.2942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.6694  1465   164  0.92  11.89   0.96     0.95      10250.74|
|  2:  4.6694 -  3.7238  1412   154  0.93  11.89   1.02     1.02      15582.46|
|  3:  3.7238 -  3.2583  1375   152  0.88  18.22   1.03     1.04      20393.01|
|  4:  3.2583 -  2.9627  1370   159  0.84  22.02   1.01     0.98      20776.55|
|  5:  2.9627 -  2.7517  1371   151  0.82  24.17   1.00     0.97      17954.78|
|  6:  2.7517 -  2.5903  1344   149  0.80  26.17   0.98     0.90      15526.30|
|  7:  2.5903 -  2.4611  1369   152  0.82  24.31   0.99     0.94      12829.67|
|  8:  2.4611 -  2.3544  1339   147  0.81  25.18   0.97     0.91      11792.10|
|  9:  2.3544 -  2.2640  1332   153  0.83  24.06   0.99     0.93      10174.14|
| 10:  2.2640 -  2.1861  1346   150  0.82  24.49   1.00     0.95       9214.98|
| 11:  2.1861 -  2.1180  1335   148  0.82  24.30   1.00     0.95       8844.71|
| 12:  2.1180 -  2.0576  1341   141  0.80  26.38   0.99     0.98       8899.98|
| 13:  2.0576 -  2.0035   998   118  0.81  26.28   0.98     0.92       7093.74|
| 14:  2.0035 -  1.9547   233    21  0.86  21.08   0.98     0.95       5136.19|
|alpha:            min =        0.90 max =            1.04 mean =         0.96|
|beta:             min =     5136.19 max =        20776.55 mean =     13064.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.98 mean =        22.05|
|phase err.(test): min =        0.00 max =           88.75 mean =        20.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.927)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    84.87   15.96    None  None   None       |
|    all(noH): 2823   0      1.03    84.87   15.96    None  None   None       |
|    Sol.    : 438    0      3.95    74.81   39.59    None  None   None       |
|    Mac.    : 2385   0      1.03    84.87   11.62    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:     1.030 -   9.414: 1228   |   5:    42.949 -  51.333:   87        |
|      1:     9.414 -  17.797:  861   |   6:    51.333 -  59.717:   89        |
|      2:    17.797 -  26.181:  250   |   7:    59.717 -  68.101:   37        |
|      3:    26.181 -  34.565:  140   |   8:    68.101 -  76.485:   12        |
|      4:    34.565 -  42.949:  118   |   9:    76.485 -  84.869:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 361         
Filter by distance & map next to the model:
   mapped sites are within: 0.652 - 5.823
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 358 from: 361
   mapped sites are within: 0.724 - 5.823

peak=    7.290 closest distance to " CG1 VAL A 296 " =    1.615
peak=    7.178 closest distance to " O   HOH Z 390 " =    1.442
peak=    6.362 closest distance to " CB  VAL A 230 " =    1.574
peak=    6.235 closest distance to " O   ASN A 285 " =    0.993
peak=    6.205 closest distance to " O   HOH Z 130 " =    1.721
peak=    6.089 closest distance to " O   HOH Z 268 " =    1.459
peak=    5.923 closest distance to " O   HOH Z  41 " =    1.677
peak=    5.826 closest distance to " OD2 ASP A 270 " =    1.241
peak=    5.769 closest distance to " O   HOH Z 415 " =    1.485
peak=    5.652 closest distance to " CD2 LEU A   5 " =    1.610
peak=    5.526 closest distance to " OG  SER A 276 " =    1.100
peak=    5.439 closest distance to " O   HOH Z  15 " =    1.400
peak=    5.426 closest distance to " CD  ARG A 138 " =    1.075
peak=    5.367 closest distance to " O   HOH Z  46 " =    1.804
peak=    5.321 closest distance to " NH1 ARG A 138 " =    1.052
peak=    5.283 closest distance to " O   HOH Z 178 " =    2.103
peak=    5.171 closest distance to " CG  ARG A 138 " =    1.299
peak=    5.050 closest distance to " CD1 LEU A   5 " =    1.235
peak=    5.033 closest distance to " O   HOH Z 416 " =    1.717
peak=    4.968 closest distance to " O   HOH Z 245 " =    1.401
peak=    4.942 closest distance to " NH2 ARG A  24 " =    0.926
peak=    4.901 closest distance to " O   HOH Z 103 " =    0.942
peak=    4.893 closest distance to " CZ  PHE A  16 " =    1.243
peak=    4.888 closest distance to " O   PRO A 198 " =    1.529
peak=    4.838 closest distance to " O   HOH Z 375 " =    1.692
peak=    4.832 closest distance to " OD1 ASN A 249 " =    1.269
peak=    4.803 closest distance to " O   HOH Z 255 " =    1.423
peak=    4.746 closest distance to " O   HOH Z 417 " =    1.804
peak=    4.712 closest distance to " NE2 GLN A  11 " =    1.443
peak=    4.684 closest distance to " O   HOH Z 111 " =    1.508
peak=    4.672 closest distance to " O   HOH Z 159 " =    1.065
peak=    4.667 closest distance to " CB  PRO A  54 " =    1.365
peak=    4.658 closest distance to " CB  LYS A 290 " =    0.978
peak=    4.623 closest distance to " O   HOH Z 401 " =    1.951
peak=    4.620 closest distance to " CG2 THR A 279 " =    1.399
peak=    4.602 closest distance to " NZ ALYS A 290 " =    1.304
peak=    4.591 closest distance to " O   HOH Z 424 " =    2.143
peak=    4.555 closest distance to " O   HOH Z  63 " =    1.857
peak=    4.543 closest distance to " O   HOH Z 139 " =    1.810
peak=    4.541 closest distance to " O   HOH Z  19 " =    2.587
peak=    4.534 closest distance to " CB  ASN A  60 " =    1.073
peak=    4.446 closest distance to " O   HOH Z  59 " =    2.219
peak=    4.409 closest distance to " CB  ARG A 275 " =    1.248
peak=    4.404 closest distance to " O   HOH Z 411 " =    3.033
peak=    4.400 closest distance to " O   HOH Z 232 " =    2.051
peak=    4.390 closest distance to " NH1AARG A 145 " =    1.214
peak=    4.386 closest distance to " O   HOH Z 289 " =    1.434
peak=    4.367 closest distance to " N   SER A  26 " =    0.930
peak=    4.348 closest distance to " NH1 ARG A  24 " =    0.932
peak=    4.336 closest distance to " ND2 ASN A 285 " =    1.131
peak=    4.319 closest distance to " NH1 ARG A  56 " =    1.483
peak=    4.315 closest distance to " CA  PRO A  54 " =    0.984
peak=    4.314 closest distance to " CE  MET A  93 " =    1.530
peak=    4.307 closest distance to " CZ  PHE A 218 " =    1.250
peak=    4.302 closest distance to " O   HOH Z 144 " =    1.840
peak=    4.291 closest distance to " O   HOH Z  70 " =    1.092
peak=    4.284 closest distance to " O   HOH Z  65 " =    1.921
peak=    4.283 closest distance to " O   HOH Z   9 " =    2.486
peak=    4.264 closest distance to " CB  SER A 216 " =    1.181
peak=    4.254 closest distance to " O   HOH Z  33 " =    1.825
peak=    4.235 closest distance to " O   HOH Z  61 " =    1.433
peak=    4.233 closest distance to " O   HOH Z 359 " =    1.429
peak=    4.224 closest distance to " O   HOH Z 350 " =    1.995
peak=    4.223 closest distance to " O   HOH Z  81 " =    1.033
peak=    4.187 closest distance to " OD1 ASP A 298 " =    1.228
peak=    4.165 closest distance to " CA  VAL A 153 " =    1.003
peak=    4.133 closest distance to " CZ  PHE A  16 " =    1.222
peak=    4.132 closest distance to " CB  SER A 210 " =    1.152
peak=    4.113 closest distance to " NE2 HIS A 207 " =    1.055
peak=    4.085 closest distance to " OD2 ASP A 140 " =    1.035
peak=    4.083 closest distance to " O   HOH Z 410 " =    2.213
peak=    4.061 closest distance to " OD1 ASN A  45 " =    1.466
peak=    4.056 closest distance to " CA  ASP A  50 " =    1.146
peak=    4.054 closest distance to " CB  ASN A 285 " =    1.223
peak=    4.045 closest distance to " CG2 THR A 251 " =    1.653
peak=    4.045 closest distance to " O   HOH Z 215 " =    1.718
peak=    4.044 closest distance to " CA  VAL A 230 " =    1.353
peak=    4.040 closest distance to " CD1AILE A 234 " =    1.209
peak=    4.034 closest distance to " O   HOH Z 374 " =    1.340
peak=    3.993 closest distance to " O   HOH Z  84 " =    1.068
peak=    3.967 closest distance to " CA  SER A  12 " =    1.571
peak=    3.952 closest distance to " CG  GLN A  88 " =    0.806
peak=    3.951 closest distance to " O   HOH Z 395 " =    1.435
peak=    3.947 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.941 closest distance to " N   CYS A 260 " =    1.208
peak=    3.940 closest distance to " OE1 GLN A  88 " =    0.935
peak=    3.931 closest distance to " O   HOH Z  57 " =    1.864
peak=    3.929 closest distance to " O   HOH Z 316 " =    3.177
peak=    3.923 closest distance to " O   HOH Z  52 " =    1.237
peak=    3.917 closest distance to " CA  SER A  87 " =    0.850
peak=    3.878 closest distance to " CB  ASN A  60 " =    1.006
peak=    3.872 closest distance to " CA  GLU A  46 " =    0.864
peak=    3.871 closest distance to " O   HOH Z 120 " =    1.206
peak=    3.871 closest distance to " CB  ASN A 187 " =    1.110
peak=    3.869 closest distance to " O   HOH Z 428 " =    1.224
peak=    3.857 closest distance to " CD1 LEU A 167 " =    1.415
peak=    3.853 closest distance to " CE3 TRP A 274 " =    1.523
peak=    3.847 closest distance to " O   HOH Z 369 " =    1.318
peak=    3.844 closest distance to " O   HOH Z  97 " =    1.913
peak=    3.837 closest distance to " OD2 ASP A  27 " =    1.002
peak=    3.833 closest distance to " O   HOH Z 144 " =    1.833
peak=    3.830 closest distance to " O   HOH Z 428 " =    1.663
peak=    3.827 closest distance to " O   HOH Z 225 " =    1.831
peak=    3.819 closest distance to " O   HOH Z  69 " =    1.798
peak=    3.815 closest distance to " O   HOH Z 183 " =    1.592
peak=    3.808 closest distance to " O   HOH Z 117 " =    1.256
peak=    3.807 closest distance to " CB  ASN A  39 " =    0.960
peak=    3.804 closest distance to " O   HOH Z  15 " =    2.158
peak=    3.804 closest distance to " CB  PRO A  54 " =    1.383
peak=    3.803 closest distance to " CE AMET A  47 " =    1.602
peak=    3.795 closest distance to " CG2 THR A 221 " =    1.369
peak=    3.775 closest distance to " O   HOH Z 368 " =    1.471
peak=    3.769 closest distance to " O   HOH Z  30 " =    1.475
peak=    3.765 closest distance to " O   HOH Z 293 " =    1.338
peak=    3.763 closest distance to " O   HOH Z  68 " =    1.980
peak=    3.751 closest distance to " CA  LEU A 282 " =    0.880
peak=    3.742 closest distance to " O   HOH Z  49 " =    1.160
peak=    3.735 closest distance to " CG2 THR A 246 " =    1.758
peak=    3.727 closest distance to " O   HOH Z 427 " =    2.457
peak=    3.726 closest distance to " O   HOH Z 287 " =    1.917
peak=    3.725 closest distance to " CB  MET A  40 " =    0.820
peak=    3.721 closest distance to " O   HOH Z 258 " =    1.311
peak=    3.718 closest distance to " OD2 ASP A  50 " =    1.082
peak=    3.717 closest distance to " CB  SER A  26 " =    1.372
peak=    3.711 closest distance to " CD  PRO A 243 " =    1.439
peak=    3.697 closest distance to " O   HOH Z  91 " =    2.156
peak=    3.688 closest distance to " O   HOH Z 154 " =    1.926
peak=    3.687 closest distance to " O   HOH Z 218 " =    2.337
peak=    3.680 closest distance to " O   HOH Z 186 " =    1.871
peak=    3.677 closest distance to " CG2 ILE A  20 " =    1.540
peak=    3.674 closest distance to " O   HOH Z 112 " =    1.468
peak=    3.671 closest distance to " O   HOH Z 233 " =    1.428
peak=    3.665 closest distance to " O   HOH Z 411 " =    1.592
peak=    3.662 closest distance to " O   HOH Z 126 " =    2.442
peak=    3.657 closest distance to " NH2BARG A 190 " =    1.489
peak=    3.655 closest distance to " O   HOH Z 385 " =    1.209
peak=    3.651 closest distance to " N   LYS A 290 " =    1.290
peak=    3.651 closest distance to " N   TYR A  15 " =    0.966
peak=    3.650 closest distance to " O   HOH Z 426 " =    1.029
peak=    3.644 closest distance to " ND2BASN A 224 " =    0.932
peak=    3.638 closest distance to " O   HOH Z 158 " =    2.637
peak=    3.636 closest distance to " O   HOH Z  27 " =    1.196
peak=    3.636 closest distance to " N   GLY A 287 " =    0.838
peak=    3.628 closest distance to " O   HOH Z 317 " =    2.581
peak=    3.626 closest distance to " O   HOH Z  78 " =    1.830
peak=    3.619 closest distance to " N   GLY A 302 " =    1.015
peak=    3.619 closest distance to " O   HOH Z  43 " =    1.392
peak=    3.617 closest distance to " CG  LYS A 166 " =    1.400
peak=    3.596 closest distance to " O   HOH Z 239 " =    1.457
peak=    3.595 closest distance to " CA  ASN A 285 " =    1.277
peak=    3.592 closest distance to " CB  ASN A 148 " =    1.263
peak=    3.586 closest distance to " CA  ALA A  51 " =    1.011
peak=    3.585 closest distance to " NH2 ARG A 269 " =    0.848
peak=    3.584 closest distance to " O   HOH Z  48 " =    1.595
peak=    3.584 closest distance to " O   HOH Z 350 " =    1.307
peak=    3.578 closest distance to " CB  SER A  63 " =    1.399
peak=    3.576 closest distance to " O   HOH Z 363 " =    1.198
peak=    3.552 closest distance to " CB  GLU A 152 " =    1.256
peak=    3.552 closest distance to " CE2 TYR A 186 " =    0.971
peak=    3.551 closest distance to " N   ASN A 142 " =    1.115
peak=    3.551 closest distance to " O   HOH Z 362 " =    4.804
peak=    3.546 closest distance to " O   HOH Z 392 " =    1.357
peak=    3.535 closest distance to " OD1 ASP A  65 " =    1.890
peak=    3.535 closest distance to " O   HOH Z 343 " =    1.855
peak=    3.534 closest distance to " O   HOH Z 172 " =    1.705
peak=    3.533 closest distance to " O   HOH Z 368 " =    1.803
peak=    3.523 closest distance to " O   HOH Z 413 " =    2.163
peak=    3.517 closest distance to " NZ  LYS A 119 " =    2.853
peak=    3.517 closest distance to " CB  ALA A  10 " =    1.275
peak=    3.512 closest distance to " CD2 TRP A 179 " =    2.238
peak=    3.506 closest distance to " N   MET A 185 " =    1.431
peak=    3.503 closest distance to " CB  GLU A   2 " =    1.086
peak=    3.493 closest distance to " O   HOH Z 116 " =    1.494
peak=    3.490 closest distance to " O   ARG A  14 " =    1.134
peak=    3.484 closest distance to " CD  GLN A 240 " =    1.763
peak=    3.480 closest distance to " NZ  LYS A 117 " =    1.506
peak=    3.479 closest distance to " O   HOH Z 119 " =    1.586
peak=    3.478 closest distance to " O   HOH Z 148 " =    2.620
peak=    3.477 closest distance to " O   HOH Z 244 " =    1.784
peak=    3.476 closest distance to " O   HOH Z 357 " =    1.690
peak=    3.471 closest distance to " O   HOH Z  26 " =    1.871
peak=    3.470 closest distance to " N   SER A  63 " =    0.892
peak=    3.467 closest distance to " CG  ASN A 249 " =    1.011
peak=    3.464 closest distance to " CG1 ILE A 120 " =    1.398
peak=    3.463 closest distance to " O   HOH Z  85 " =    1.726
peak=    3.462 closest distance to " O   HOH Z 118 " =    2.668
peak=    3.462 closest distance to " CG2 ILE A 151 " =    0.914
peak=    3.458 closest distance to " CG2 THR A 294 " =    1.241
peak=    3.457 closest distance to " O   THR A 220 " =    1.878
peak=    3.452 closest distance to " OD1 ASN A  69 " =    2.943
peak=    3.450 closest distance to " O   HOH Z 434 " =    1.576
peak=    3.447 closest distance to " O   HOH Z 222 " =    1.767
peak=    3.443 closest distance to " O   HOH Z  57 " =    1.928
peak=    3.438 closest distance to " O   HOH Z 138 " =    0.900
peak=    3.437 closest distance to " O   HOH Z 381 " =    1.081
peak=    3.437 closest distance to " O   HOH Z 361 " =    1.732
peak=    3.436 closest distance to " O   HOH Z 239 " =    1.646
peak=    3.434 closest distance to " O   HOH Z 148 " =    2.109
peak=    3.431 closest distance to " CG1AVAL A  72 " =    1.442
peak=    3.429 closest distance to " CA  GLY A 136 " =    1.080
peak=    3.428 closest distance to " CE1 PHE A 225 " =    1.111
peak=    3.425 closest distance to " O   THR A 294 " =    0.879
peak=    3.420 closest distance to " CD ALYS A 290 " =    1.092
peak=    3.419 closest distance to " O   GLY A 302 " =    1.484
peak=    3.418 closest distance to " O   HOH Z 266 " =    1.770
peak=    3.418 closest distance to " CB  PHE A 225 " =    1.592
peak=    3.418 closest distance to " CG  GLN A  89 " =    1.631
peak=    3.417 closest distance to " O   HOH Z 215 " =    3.173
peak=    3.416 closest distance to " CA  ALA A 295 " =    1.077
peak=    3.411 closest distance to " CG  PRO A 243 " =    1.072
peak=    3.411 closest distance to " OD1 ASP A 298 " =    1.968
peak=    3.407 closest distance to " O   HOH Z 139 " =    2.473
peak=    3.403 closest distance to " CB  TYR A 169 " =    0.749
peak=    3.402 closest distance to " O   HOH Z  39 " =    3.918
peak=    3.400 closest distance to " N   GLN A  73 " =    1.159
peak=    3.399 closest distance to " CZ AARG A 190 " =    1.980
peak=    3.399 closest distance to " O   HOH Z 261 " =    2.310
peak=    3.397 closest distance to " CG  PRO A 198 " =    1.595
peak=    3.397 closest distance to " N   SER A  97 " =    0.886
peak=    3.396 closest distance to " OG BSER A 258 " =    1.139
peak=    3.395 closest distance to " O   HOH Z 158 " =    2.722
peak=    3.394 closest distance to " O   HOH Z 230 " =    1.379
peak=    3.391 closest distance to " CA  THR A  42 " =    1.086
peak=    3.386 closest distance to " N   ALA A 165 " =    1.396
peak=    3.379 closest distance to " O   HOH Z  35 " =    4.436
peak=    3.379 closest distance to " C   GLN A  73 " =    1.179
peak=    3.376 closest distance to " O   ASN A  60 " =    1.184
peak=    3.373 closest distance to " CA  ILE A 234 " =    1.293
peak=    3.366 closest distance to " CB  VAL A 202 " =    1.493
peak=    3.363 closest distance to " CB  ASN A 284 " =    0.933
peak=    3.363 closest distance to " CA  GLY A 262 " =    1.590
peak=    3.361 closest distance to " CB  SER A   3 " =    1.636
peak=    3.361 closest distance to " CB  ARG A 138 " =    1.127
peak=    3.361 closest distance to " O   HOH Z 133 " =    1.304
peak=    3.360 closest distance to " O   HOH Z  69 " =    1.337
peak=    3.360 closest distance to " O   HOH Z 153 " =    4.023
peak=    3.355 closest distance to " N   VAL A 296 " =    1.971
peak=    3.354 closest distance to " O   HOH Z 418 " =    0.996
peak=    3.354 closest distance to " O   HOH Z  39 " =    1.800
peak=    3.346 closest distance to " O   HOH Z 181 " =    2.488
peak=    3.345 closest distance to " CB  ASP A 298 " =    1.084
peak=    3.342 closest distance to " O   HOH Z 178 " =    1.400
peak=    3.341 closest distance to " O   HOH Z 287 " =    2.121
peak=    3.340 closest distance to " O   HOH Z  80 " =    1.564
peak=    3.340 closest distance to " OG BSER A 164 " =    2.480
peak=    3.338 closest distance to " CD1 LEU A 261 " =    1.501
peak=    3.330 closest distance to " CA  THR A 182 " =    0.928
peak=    3.330 closest distance to " ND1 HIS A  81 " =    1.709
peak=    3.329 closest distance to " N   GLN A 278 " =    0.866
peak=    3.325 closest distance to " O   HOH Z 422 " =    1.100
peak=    3.321 closest distance to " CG2 ILE A 239 " =    1.979
peak=    3.320 closest distance to " CD  ARG A  56 " =    0.970
peak=    3.318 closest distance to " CB  GLU A 236 " =    1.269
peak=    3.318 closest distance to " CA  ASP A 149 " =    1.358
peak=    3.317 closest distance to " CB  ASP A 124 " =    0.859
peak=    3.311 closest distance to " O   HOH Z 425 " =    1.534
peak=    3.311 closest distance to " CG1BVAL A  72 " =    1.309
peak=    3.311 closest distance to " O   HOH Z 128 " =    1.903
peak=    3.307 closest distance to " O   HOH Z 362 " =    1.980
peak=    3.305 closest distance to " OXT GLY A 302 " =    2.434
peak=    3.302 closest distance to " O   HOH Z 369 " =    1.964
peak=    3.301 closest distance to " O   HOH Z 294 " =    1.698
peak=    3.300 closest distance to " O   SER A 288 " =    1.105
peak=    3.299 closest distance to " N   SER A 210 " =    0.920
peak=    3.297 closest distance to " CD2 LEU A 297 " =    0.995
peak=    3.290 closest distance to " CB  ALA A  21 " =    1.153
peak=    3.289 closest distance to " O   HOH Z  19 " =    2.299
peak=    3.289 closest distance to " CD2 LEU A 228 " =    1.390
peak=    3.288 closest distance to " O   HOH Z 423 " =    1.244
peak=    3.287 closest distance to " O   HOH Z 295 " =    1.385
peak=    3.285 closest distance to " CB  ALA A  43 " =    1.332
peak=    3.283 closest distance to " CE3 TRP A  85 " =    1.000
peak=    3.282 closest distance to " O   HOH Z 298 " =    2.299
peak=    3.282 closest distance to " NE2 GLN A  58 " =    5.823
peak=    3.282 closest distance to " O   GLY A 211 " =    1.200
peak=    3.281 closest distance to " CA  ALA A 180 " =    1.479
peak=    3.281 closest distance to " CB  ARG A 259 " =    1.848
peak=    3.280 closest distance to " CH2 TRP A 150 " =    1.211
peak=    3.277 closest distance to " NH1BARG A 145 " =    2.141
peak=    3.276 closest distance to " CB  ARG A 156 " =    1.268
peak=    3.273 closest distance to " CG  GLU A   2 " =    1.088
peak=    3.268 closest distance to " O   HOH Z 279 " =    2.738
peak=    3.268 closest distance to " O   HOH Z 167 " =    1.677
peak=    3.267 closest distance to " O   HOH Z 112 " =    1.300
peak=    3.266 closest distance to " CB  THR A   4 " =    1.027
peak=    3.265 closest distance to " CB  SER A 271 " =    1.228
peak=    3.263 closest distance to " OD2 ASP A 286 " =    2.648
peak=    3.256 closest distance to " CA  MET A  47 " =    1.141
peak=    3.256 closest distance to " O   HOH Z 185 " =    1.547
peak=    3.255 closest distance to " CG  LEU A 228 " =    1.334
peak=    3.243 closest distance to " CB  PRO A  90 " =    1.445
peak=    3.243 closest distance to " CD  LYS A  76 " =    1.795
peak=    3.241 closest distance to " N   SER A 134 " =    0.803
peak=    3.234 closest distance to " O   HOH Z 386 " =    2.251
peak=    3.232 closest distance to " O   HOH Z 371 " =    2.031
peak=    3.232 closest distance to " O   HOH Z 389 " =    1.331
peak=    3.230 closest distance to " CA  ARG A 159 " =    1.524
peak=    3.230 closest distance to " O   HOH Z 104 " =    1.807
peak=    3.229 closest distance to " C   GLN A  11 " =    1.379
peak=    3.227 closest distance to " CG2 THR A  82 " =    1.179
peak=    3.226 closest distance to " N   ALA A 161 " =    1.280
peak=    3.224 closest distance to " NH1BARG A 102 " =    1.778
peak=    3.224 closest distance to " O   HOH Z 325 " =    1.873
peak=    3.219 closest distance to " CB  SER A  62 " =    1.309
peak=    3.218 closest distance to " O   ALA A 165 " =    1.414
peak=    3.217 closest distance to " OG  SER A  28 " =    1.706
peak=    3.216 closest distance to " O   HOH Z 214 " =    1.453
peak=    3.216 closest distance to " CA  ALA A 299 " =    0.900
peak=    3.214 closest distance to " CB  LEU A  83 " =    0.750
peak=    3.208 closest distance to " C   ASN A 209 " =    1.451
peak=    3.207 closest distance to " CG2 ILE A 109 " =    0.998
peak=    3.197 closest distance to " O   HOH Z  96 " =    2.050
peak=    3.194 closest distance to " N   ASN A  74 " =    0.810
peak=    3.193 closest distance to " CA  ILE A  49 " =    0.907
peak=    3.191 closest distance to " CG  ARG A 159 " =    0.724
peak=    3.191 closest distance to " CA  LEU A 222 " =    1.124
peak=    3.188 closest distance to " O   HOH Z 424 " =    3.086
peak=    3.179 closest distance to " CB  ALA A 248 " =    1.696
peak=    3.176 closest distance to " OD1 ASN A 217 " =    1.488
peak=    3.176 closest distance to " O   HOH Z 171 " =    1.601
peak=    3.176 closest distance to " CG2 VAL A 296 " =    1.023
peak=    3.173 closest distance to " O   HOH Z 380 " =    4.915
peak=    3.170 closest distance to " CG  LEU A 167 " =    1.423
peak=    3.170 closest distance to " O   HOH Z 118 " =    4.005
peak=    3.169 closest distance to " CG2 ILE A 234 " =    1.743
peak=    3.166 closest distance to " CA  GLY A 118 " =    0.756
peak=    3.165 closest distance to " O   HOH Z 238 " =    2.277
peak=    3.163 closest distance to " O   HOH Z 132 " =    1.822
peak=    3.163 closest distance to " O   HOH Z 265 " =    1.894
peak=    3.161 closest distance to " O   HOH Z 246 " =    1.494
peak=    3.160 closest distance to " CA  TRP A  92 " =    1.523
peak=    3.158 closest distance to " CG BARG A 102 " =    2.081
peak=    3.156 closest distance to " O   HOH Z 168 " =    1.923
peak=    3.151 closest distance to " O   HOH Z 373 " =    1.743
peak=    3.151 closest distance to " CB  GLN A 103 " =    1.375
peak=    3.148 closest distance to " CB  TRP A 179 " =    1.402
peak=    3.146 closest distance to " NH2AARG A 145 " =    1.092
peak=    3.140 closest distance to " ND2 ASN A 284 " =    1.018
peak=    3.138 closest distance to " CB  GLN A  73 " =    0.991
peak=    3.137 closest distance to " CA  ARG A 195 " =    1.438
peak=    3.131 closest distance to " NH2AARG A 102 " =    1.156
peak=    3.130 closest distance to " NH1BARG A 275 " =    1.510
peak=    3.128 closest distance to " CB  SER A 212 " =    1.208
peak=    3.128 closest distance to " O   HOH Z  24 " =    1.628
peak=    3.126 closest distance to " N   TYR A 293 " =    0.964
peak=    3.125 closest distance to " O   HOH Z 286 " =    1.818
peak=    3.125 closest distance to " CB  MET A  93 " =    1.784
peak=    3.119 closest distance to " O   HOH Z 196 " =    1.132
peak=    3.118 closest distance to " CA  THR A  42 " =    0.990
peak=    3.115 closest distance to " O   HOH Z 284 " =    2.630
peak=    3.108 closest distance to " CA  TYR A  30 " =    1.162
peak=    3.104 closest distance to " O   HOH Z 147 " =    1.789
peak=    3.099 closest distance to " O   HOH Z 217 " =    2.966
peak=    3.096 closest distance to " OE1 GLU A   2 " =    1.732
peak=    3.093 closest distance to " O   HOH Z 258 " =    3.369
peak=    3.093 closest distance to " CB  ALA A 137 " =    0.924
peak=    3.030 closest distance to " N   THR A 294 " =    1.169
peak=    3.024 closest distance to " O   HOH Z 113 " =    1.913

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 238         
Filter by distance & map next to the model:
   mapped sites are within: 0.175 - 5.588
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 238
   mapped sites are within: 0.700 - 5.588

peak=   -5.272 closest distance to " O   ASN A 285 " =    0.974
peak=   -5.160 closest distance to " CD  ARG A 138 " =    0.974
peak=   -4.872 closest distance to " O   HOH Z 313 " =    0.945
peak=   -4.821 closest distance to " O   THR A 178 " =    0.819
peak=   -4.808 closest distance to " O   HOH Z 163 " =    1.026
peak=   -4.672 closest distance to " OG  SER A  63 " =    1.063
peak=   -4.493 closest distance to " CG2 VAL A 230 " =    0.843
peak=   -4.391 closest distance to " O   HOH Z 404 " =    0.879
peak=   -4.314 closest distance to " N   ARG A 275 " =    1.262
peak=   -4.310 closest distance to " O   HOH Z 117 " =    0.856
peak=   -4.294 closest distance to " C   ASP A  50 " =    1.216
peak=   -4.220 closest distance to " CD  GLU A 277 " =    0.794
peak=   -4.205 closest distance to " O   PRO A 198 " =    1.024
peak=   -4.176 closest distance to " N   THR A  29 " =    1.180
peak=   -4.122 closest distance to " O   ALA A 226 " =    1.438
peak=   -4.115 closest distance to " CZ  ARG A  24 " =    2.172
peak=   -4.109 closest distance to " CB  ASN A 285 " =    2.092
peak=   -4.072 closest distance to " N   GLY A 287 " =    0.975
peak=   -4.057 closest distance to " O   HOH Z 216 " =    1.188
peak=   -4.022 closest distance to " OD1 ASN A 249 " =    1.101
peak=   -4.022 closest distance to " OE1 GLN A  88 " =    0.881
peak=   -4.009 closest distance to " NH1 ARG A 138 " =    1.000
peak=   -3.967 closest distance to " O   HOH Z 268 " =    0.800
peak=   -3.962 closest distance to " OG  SER A  97 " =    1.906
peak=   -3.951 closest distance to " CB  PHE A 130 " =    1.073
peak=   -3.949 closest distance to " CD  ARG A  14 " =    3.070
peak=   -3.944 closest distance to " O   HOH Z  52 " =    1.420
peak=   -3.941 closest distance to " CD2 LEU A   5 " =    0.848
peak=   -3.940 closest distance to " O   HOH Z 290 " =    1.150
peak=   -3.927 closest distance to " O   HOH Z 316 " =    2.010
peak=   -3.926 closest distance to " CG  ASP A 270 " =    0.886
peak=   -3.910 closest distance to " O   ASP A 286 " =    0.937
peak=   -3.878 closest distance to " NH2 ARG A  24 " =    0.863
peak=   -3.853 closest distance to " O   MET A  47 " =    2.634
peak=   -3.848 closest distance to " O   VAL A 174 " =    2.225
peak=   -3.843 closest distance to " CG  MET A 105 " =    0.989
peak=   -3.830 closest distance to " CG  GLN A  88 " =    0.920
peak=   -3.819 closest distance to " OD1 ASP A 298 " =    1.008
peak=   -3.805 closest distance to " O   HOH Z 103 " =    0.895
peak=   -3.777 closest distance to " O   HOH Z  32 " =    1.619
peak=   -3.764 closest distance to " O   HOH Z 133 " =    1.234
peak=   -3.760 closest distance to " O   HOH Z 186 " =    1.494
peak=   -3.759 closest distance to " CD1 TRP A 274 " =    1.116
peak=   -3.746 closest distance to " CD2 TYR A 116 " =    2.107
peak=   -3.726 closest distance to " CD2 TRP A 150 " =    1.292
peak=   -3.723 closest distance to " C   PHE A  59 " =    0.871
peak=   -3.706 closest distance to " CG  ASN A 284 " =    1.058
peak=   -3.695 closest distance to " NH1 ARG A  24 " =    0.884
peak=   -3.674 closest distance to " O   ALA A  51 " =    1.435
peak=   -3.671 closest distance to " CG  PRO A 213 " =    2.185
peak=   -3.669 closest distance to " C   PHE A 155 " =    1.145
peak=   -3.667 closest distance to " OG BSER A 134 " =    2.230
peak=   -3.666 closest distance to " CB  ASP A  27 " =    2.715
peak=   -3.665 closest distance to " OD2 ASP A  50 " =    0.988
peak=   -3.653 closest distance to " O   HOH Z 354 " =    2.827
peak=   -3.640 closest distance to " OD1 ASP A  27 " =    1.258
peak=   -3.638 closest distance to " CA  GLY A 241 " =    2.177
peak=   -3.634 closest distance to " O   HOH Z 211 " =    1.125
peak=   -3.633 closest distance to " OD2 ASP A 272 " =    1.519
peak=   -3.631 closest distance to " O   HOH Z 435 " =    2.494
peak=   -3.622 closest distance to " OE2 GLU A 152 " =    1.174
peak=   -3.618 closest distance to " ND2 ASN A 285 " =    1.260
peak=   -3.615 closest distance to " O   SER A   3 " =    2.268
peak=   -3.608 closest distance to " CB  ASP A  27 " =    1.089
peak=   -3.599 closest distance to " O   HOH Z  60 " =    1.503
peak=   -3.599 closest distance to " CG  LEU A 228 " =    0.907
peak=   -3.595 closest distance to " CA  ASN A 284 " =    0.970
peak=   -3.591 closest distance to " O   HOH Z  73 " =    2.237
peak=   -3.581 closest distance to " O   SER A 135 " =    1.555
peak=   -3.572 closest distance to " CD  LYS A 289 " =    2.264
peak=   -3.568 closest distance to " CA  GLY A  98 " =    2.158
peak=   -3.564 closest distance to " NH2AARG A 275 " =    5.588
peak=   -3.556 closest distance to " O   HOH Z 244 " =    1.823
peak=   -3.551 closest distance to " CG2 ILE A 120 " =    0.851
peak=   -3.550 closest distance to " CG BMET A  47 " =    1.071
peak=   -3.544 closest distance to " CB  VAL A 125 " =    1.910
peak=   -3.543 closest distance to " OD1 ASP A 171 " =    1.624
peak=   -3.531 closest distance to " O   HOH Z 428 " =    1.169
peak=   -3.528 closest distance to " O   HOH Z 155 " =    0.901
peak=   -3.526 closest distance to " OE1 GLU A  44 " =    1.277
peak=   -3.520 closest distance to " O   HOH Z 403 " =    1.140
peak=   -3.518 closest distance to " CB  ASN A  60 " =    1.098
peak=   -3.514 closest distance to " OE2 GLU A 277 " =    3.575
peak=   -3.503 closest distance to " O   VAL A 125 " =    2.225
peak=   -3.495 closest distance to " OG1 THR A 157 " =    1.187
peak=   -3.494 closest distance to " C   SER A 276 " =    1.795
peak=   -3.493 closest distance to " C   MET A 188 " =    1.687
peak=   -3.492 closest distance to " OG  SER A  32 " =    1.744
peak=   -3.485 closest distance to " OE2 GLU A 277 " =    2.671
peak=   -3.480 closest distance to " CB  ASN A  39 " =    2.338
peak=   -3.470 closest distance to " O   HOH Z  54 " =    0.875
peak=   -3.461 closest distance to " OD1 ASP A 107 " =    1.334
peak=   -3.455 closest distance to " OD2 ASP A 140 " =    0.932
peak=   -3.454 closest distance to " O   SER A 271 " =    1.689
peak=   -3.445 closest distance to " O   HOH Z  70 " =    2.125
peak=   -3.445 closest distance to " N   ALA A 242 " =    0.956
peak=   -3.441 closest distance to " O   HOH Z 257 " =    1.092
peak=   -3.436 closest distance to " O   HOH Z 350 " =    2.310
peak=   -3.428 closest distance to " CE1 TYR A 247 " =    2.575
peak=   -3.413 closest distance to " O   HOH Z 389 " =    0.729
peak=   -3.412 closest distance to " CE3 TRP A 179 " =    1.201
peak=   -3.412 closest distance to " CG1 VAL A  78 " =    2.305
peak=   -3.401 closest distance to " O   HOH Z 177 " =    2.680
peak=   -3.401 closest distance to " ND2 ASN A 285 " =    2.022
peak=   -3.397 closest distance to " O   HOH Z 111 " =    1.810
peak=   -3.393 closest distance to " SG BCYS A 201 " =    0.759
peak=   -3.389 closest distance to " O   HOH Z 251 " =    4.652
peak=   -3.387 closest distance to " O   HOH Z 385 " =    1.193
peak=   -3.385 closest distance to " CG  ARG A 139 " =    1.714
peak=   -3.382 closest distance to " OD2 ASP A 270 " =    0.700
peak=   -3.375 closest distance to " CE2 TYR A  30 " =    2.479
peak=   -3.370 closest distance to " O   SER A  22 " =    2.820
peak=   -3.369 closest distance to " N   TYR A  68 " =    2.616
peak=   -3.364 closest distance to " OD2 ASP A 140 " =    0.810
peak=   -3.364 closest distance to " OG  SER A  87 " =    1.209
peak=   -3.361 closest distance to " NE2 GLN A 223 " =    1.486
peak=   -3.360 closest distance to " O   HOH Z 147 " =    0.982
peak=   -3.359 closest distance to " CD2 LEU A 237 " =    2.544
peak=   -3.356 closest distance to " O   GLY A  91 " =    1.631
peak=   -3.347 closest distance to " CG  LEU A   5 " =    0.901
peak=   -3.346 closest distance to " OG  SER A  87 " =    1.599
peak=   -3.344 closest distance to " O   LYS A 193 " =    1.666
peak=   -3.344 closest distance to " OE1 GLN A 278 " =    1.129
peak=   -3.343 closest distance to " NE1 TRP A 179 " =    0.755
peak=   -3.330 closest distance to " O   HOH Z 329 " =    0.989
peak=   -3.329 closest distance to " NE2 GLN A  58 " =    3.177
peak=   -3.326 closest distance to " CB  ASP A  50 " =    2.216
peak=   -3.325 closest distance to " O   PHE A 218 " =    1.739
peak=   -3.319 closest distance to " CG2 ILE A 151 " =    2.423
peak=   -3.318 closest distance to " N   PHE A 218 " =    0.909
peak=   -3.316 closest distance to " OE1 GLN A  11 " =    0.933
peak=   -3.307 closest distance to " CB  ALA A 248 " =    2.229
peak=   -3.306 closest distance to " O   TRP A  70 " =    1.400
peak=   -3.306 closest distance to " CB  ALA A   9 " =    2.777
peak=   -3.302 closest distance to " CD1 ILE A  33 " =    2.538
peak=   -3.295 closest distance to " O   HOH Z 286 " =    1.775
peak=   -3.294 closest distance to " O   THR A 279 " =    0.815
peak=   -3.292 closest distance to " OE1 GLN A  77 " =    1.007
peak=   -3.287 closest distance to " O   HOH Z  60 " =    1.375
peak=   -3.286 closest distance to " C   SER A 135 " =    1.121
peak=   -3.284 closest distance to " CD  GLN A  88 " =    1.245
peak=   -3.282 closest distance to " O   HOH Z 384 " =    0.878
peak=   -3.277 closest distance to " O   HOH Z 209 " =    2.476
peak=   -3.277 closest distance to " O   HOH Z 372 " =    1.490
peak=   -3.274 closest distance to " CA  ASN A 285 " =    1.088
peak=   -3.273 closest distance to " OG  SER A  28 " =    1.678
peak=   -3.271 closest distance to " CA  ILE A 120 " =    1.313
peak=   -3.260 closest distance to " CD1 PHE A  59 " =    1.570
peak=   -3.257 closest distance to " N   GLN A  55 " =    1.395
peak=   -3.257 closest distance to " O   HOH Z  37 " =    2.247
peak=   -3.256 closest distance to " O   HOH Z 434 " =    4.533
peak=   -3.255 closest distance to " O   HOH Z 172 " =    2.464
peak=   -3.254 closest distance to " CG2 THR A  31 " =    2.264
peak=   -3.253 closest distance to " C   VAL A  72 " =    0.862
peak=   -3.247 closest distance to " CD2 LEU A 237 " =    2.070
peak=   -3.246 closest distance to " CA  GLY A  57 " =    2.253
peak=   -3.243 closest distance to " ND2BASN A 224 " =    1.389
peak=   -3.240 closest distance to " CB  ALA A 291 " =    1.520
peak=   -3.237 closest distance to " O   HOH Z 368 " =    0.769
peak=   -3.236 closest distance to " O   HOH Z 135 " =    0.905
peak=   -3.232 closest distance to " CD  GLN A 122 " =    1.240
peak=   -3.231 closest distance to " O   HOH Z 282 " =    4.347
peak=   -3.227 closest distance to " O   HOH Z  78 " =    0.807
peak=   -3.224 closest distance to " CZ  PHE A  16 " =    0.794
peak=   -3.223 closest distance to " ND2 ASN A 173 " =    2.236
peak=   -3.216 closest distance to " O   HOH Z  27 " =    0.979
peak=   -3.215 closest distance to " O   THR A  82 " =    1.180
peak=   -3.214 closest distance to " OE1 GLN A  88 " =    1.317
peak=   -3.206 closest distance to " O   HOH Z 166 " =    1.790
peak=   -3.197 closest distance to " O   HOH Z 416 " =    1.119
peak=   -3.197 closest distance to " O   HOH Z  15 " =    1.031
peak=   -3.196 closest distance to " O   HOH Z  86 " =    0.840
peak=   -3.187 closest distance to " CG  ARG A  66 " =    1.393
peak=   -3.187 closest distance to " O   SER A  32 " =    1.589
peak=   -3.183 closest distance to " CB  PHE A  61 " =    1.242
peak=   -3.180 closest distance to " O   HOH Z  35 " =    4.663
peak=   -3.175 closest distance to " C   HIS A 108 " =    1.111
peak=   -3.174 closest distance to " CB  PHE A 218 " =    1.514
peak=   -3.170 closest distance to " CB  SER A 276 " =    1.702
peak=   -3.170 closest distance to " CG  TRP A 266 " =    1.830
peak=   -3.163 closest distance to " O   HOH Z 174 " =    2.862
peak=   -3.158 closest distance to " NE2 GLN A 194 " =    2.160
peak=   -3.156 closest distance to " O   HOH Z 386 " =    1.679
peak=   -3.151 closest distance to " CG2 ILE A  20 " =    2.741
peak=   -3.150 closest distance to " CA  TYR A  68 " =    1.188
peak=   -3.145 closest distance to " CA  MET A  47 " =    1.183
peak=   -3.141 closest distance to " O   HOH Z 113 " =    1.918
peak=   -3.140 closest distance to " NE2 GLN A  11 " =    0.964
peak=   -3.140 closest distance to " O   HOH Z 241 " =    1.265
peak=   -3.135 closest distance to " NH1 ARG A 259 " =    1.435
peak=   -3.134 closest distance to " O   HOH Z 174 " =    0.844
peak=   -3.131 closest distance to " O   GLY A 203 " =    2.261
peak=   -3.126 closest distance to " O   ASP A 140 " =    1.898
peak=   -3.120 closest distance to " C   GLU A  44 " =    1.601
peak=   -3.119 closest distance to " CG1 VAL A  78 " =    2.846
peak=   -3.119 closest distance to " O   HOH Z  81 " =    1.230
peak=   -3.117 closest distance to " O   HOH Z  81 " =    0.910
peak=   -3.117 closest distance to " O   HOH Z 159 " =    0.847
peak=   -3.111 closest distance to " O   ASN A 284 " =    1.199
peak=   -3.111 closest distance to " O   HOH Z 390 " =    2.432
peak=   -3.107 closest distance to " N   PRO A  54 " =    1.180
peak=   -3.106 closest distance to " OG  SER A 245 " =    1.593
peak=   -3.104 closest distance to " O   HOH Z  92 " =    0.886
peak=   -3.102 closest distance to " O   HOH Z  54 " =    1.223
peak=   -3.097 closest distance to " O   HOH Z 138 " =    1.205
peak=   -3.097 closest distance to " O   HOH Z 300 " =    0.808
peak=   -3.095 closest distance to " O   HOH Z  88 " =    2.008
peak=   -3.093 closest distance to " OG  SER A  32 " =    0.816
peak=   -3.090 closest distance to " O   GLY A  80 " =    2.646
peak=   -3.080 closest distance to " CB  ALA A 248 " =    2.145
peak=   -3.069 closest distance to " ND2 ASN A 249 " =    1.034
peak=   -3.068 closest distance to " N   SER A  26 " =    1.013
peak=   -3.063 closest distance to " CG  GLN A  73 " =    1.179
peak=   -3.062 closest distance to " O   HOH Z 115 " =    4.632
peak=   -3.059 closest distance to " O   HOH Z 389 " =    2.429
peak=   -3.031 closest distance to " O   SER A 141 " =    1.589
peak=   -3.029 closest distance to " CG  GLU A 277 " =    3.739
peak=   -3.025 closest distance to " OE1 GLU A  44 " =    0.966

================= 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 individual 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    :  0.5204 0.5127   6.317647e+00   6.308331e+00
   1_bss:  0.5125 0.5028   6.315748e+00   6.305159e+00
   1_xyz:  0.4616 0.4816   6.269830e+00   6.287227e+00
   1_adp:  0.4259 0.4899   6.242537e+00   6.290085e+00
   1_occ:  0.4254 0.4892   6.242058e+00   6.290187e+00
   2_bss:  0.4238 0.4883   6.242877e+00   6.289818e+00
   2_xyz:  0.3842 0.4716   6.184037e+00   6.266602e+00
   2_adp:  0.3811 0.4600   6.175318e+00   6.257095e+00
   2_occ:  0.3810 0.4595   6.174741e+00   6.256748e+00
   3_bss:  0.3816 0.4595   6.176240e+00   6.256510e+00
   3_xyz:  0.3293 0.4083   6.065514e+00   6.183769e+00
   3_adp:  0.3086 0.3996   6.030845e+00   6.166778e+00
   3_occ:  0.3083 0.3993   6.029835e+00   6.166059e+00
   4_bss:  0.3081 0.3985   6.028996e+00   6.164866e+00
   4_xyz:  0.2475 0.3285   5.848753e+00   6.030085e+00
   4_adp:  0.2191 0.2979   5.750233e+00   5.959751e+00
   4_occ:  0.2189 0.2977   5.748782e+00   5.958539e+00
   5_bss:  0.2187 0.2972   5.747316e+00   5.956693e+00
   5_xyz:  0.1775 0.2446   5.566347e+00   5.799231e+00
   5_adp:  0.1672 0.2251   5.499048e+00   5.719712e+00
   5_occ:  0.1669 0.2244   5.497461e+00   5.717998e+00
   5_bss:  0.1668 0.2233   5.495653e+00   5.713792e+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:  0.342  20.001   8.196   7.846   7.489   0.000   0.000   0.000
   1_xyz:  0.342  20.001   8.196   7.846   7.489   0.000   0.000   0.000
   1_adp:  0.342  20.001   8.196   7.846   7.489   0.000   0.000   0.000
   1_occ:  0.342  20.001   8.196   7.846   7.489   0.000   0.000   0.000
   2_bss:  0.350  50.000   4.602   3.871   3.804   0.000   0.000   0.000
   2_xyz:  0.350  50.000   4.602   3.871   3.804   0.000   0.000   0.000
   2_adp:  0.350  50.000   4.602   3.871   3.804   0.000   0.000   0.000
   2_occ:  0.350  50.000   4.602   3.871   3.804   0.000   0.000   0.000
   3_bss:  0.338  50.000   3.101   2.368   3.119   0.000   0.000   0.000
   3_xyz:  0.338  50.000   3.101   2.368   3.119   0.000   0.000   0.000
   3_adp:  0.338  50.000   3.101   2.368   3.119   0.000   0.000   0.000
   3_occ:  0.338  50.000   3.101   2.368   3.119   0.000   0.000   0.000
   4_bss:  0.353  72.099   1.742   0.981   2.108   0.000   0.000   0.000
   4_xyz:  0.353  72.099   1.742   0.981   2.108   0.000   0.000   0.000
   4_adp:  0.353  72.099   1.742   0.981   2.108   0.000   0.000   0.000
   4_occ:  0.353  72.099   1.742   0.981   2.108   0.000   0.000   0.000
   5_bss:  0.339  72.099   0.850  -0.033   1.572  -0.000   0.000   0.000
   5_xyz:  0.339  72.099   0.850  -0.033   1.572  -0.000   0.000   0.000
   5_adp:  0.339  72.099   0.850  -0.033   1.572  -0.000   0.000   0.000
   5_occ:  0.339  72.099   0.850  -0.033   1.572  -0.000   0.000   0.000
   5_bss:  0.327  55.576   0.009  -0.938   0.929  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.747 0.2929  0.3613    90773.455
   1_bss:  66.626 0.3075  0.4785    90395.274
   1_xyz:  61.837 0.3691  0.5601    80451.924
   1_adp:  63.492 0.3468  0.5929    82439.311
   1_occ:  63.435 0.3477  0.5933    82530.942
   2_bss:  63.200 0.3505  0.5315    81936.753
   2_xyz:  58.489 0.4111  0.6224    72178.261
   2_adp:  55.662 0.4479  0.6783    68121.132
   2_occ:  55.632 0.4482  0.6784    67940.801
   3_bss:  55.533 0.4495  0.6528    67844.314
   3_xyz:  46.253 0.5654  0.8134    48903.109
   3_adp:  44.334 0.5892  0.8427    46177.714
   3_occ:  44.272 0.5898  0.8426    45970.955
   4_bss:  44.072 0.5922  0.8099    45564.580
   4_xyz:  35.050 0.6992  0.9242    29980.694
   4_adp:  30.703 0.7493  0.9481    24040.617
   4_occ:  30.640 0.7500  0.9483    23932.083
   5_bss:  30.532 0.7511  0.9224    23766.479
   5_xyz:  24.918 0.8107  0.9666    15851.248
   5_adp:  22.076 0.8411  0.9824    13340.953
   5_occ:  22.024 0.8416  0.9821    13251.352
   5_bss:  21.924 0.8423  0.9567    13067.277
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3844e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3844e+01
   1_xyz:   1.772  0.014  0.111 18.651  0.007  4.103   1.5968e-01
   1_adp:   1.772  0.014  0.111 18.651  0.007  4.103   1.5968e-01
   1_occ:   1.772  0.014  0.111 18.651  0.007  4.103   1.5968e-01
   2_bss:   1.772  0.014  0.111 18.651  0.007  4.103   1.5968e-01
   2_xyz:   1.181  0.008  0.080 16.858  0.005  4.104   9.4589e-02
   2_adp:   1.181  0.008  0.080 16.858  0.005  4.104   9.4589e-02
   2_occ:   1.181  0.008  0.080 16.858  0.005  4.104   9.4589e-02
   3_bss:   1.181  0.008  0.080 16.858  0.005  4.104   9.4589e-02
   3_xyz:   1.238  0.009  0.087 16.544  0.005  4.124   1.0268e-01
   3_adp:   1.238  0.009  0.087 16.544  0.005  4.124   1.0268e-01
   3_occ:   1.238  0.009  0.087 16.544  0.005  4.124   1.0268e-01
   4_bss:   1.238  0.009  0.087 16.544  0.005  4.124   1.0268e-01
   4_xyz:   1.348  0.012  0.092 16.644  0.005  4.107   1.1695e-01
   4_adp:   1.348  0.012  0.092 16.644  0.005  4.107   1.1695e-01
   4_occ:   1.348  0.012  0.092 16.644  0.005  4.107   1.1695e-01
   5_bss:   1.348  0.012  0.092 16.644  0.005  4.107   1.1695e-01
   5_xyz:   1.144  0.009  0.082 15.648  0.004  4.119   8.0251e-02
   5_adp:   1.144  0.009  0.082 15.648  0.004  4.119   8.0251e-02
   5_occ:   1.144  0.009  0.082 15.648  0.004  4.119   8.0251e-02
   5_bss:   1.144  0.009  0.082 15.648  0.004  4.119   8.0251e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9769e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9769e+00
   1_xyz:  13.303  0.194  0.434 88.383  0.038  2.135   1.0635e-01
   1_adp:  13.303  0.194  0.434 88.383  0.038  2.135   1.0635e-01
   1_occ:  13.303  0.194  0.434 88.383  0.038  2.135   1.0635e-01
   2_bss:  13.303  0.194  0.434 88.383  0.038  2.135   1.0635e-01
   2_xyz:   6.510  0.068  0.279 85.922  0.046  1.937   5.9594e-02
   2_adp:   6.510  0.068  0.279 85.922  0.046  1.937   5.9594e-02
   2_occ:   6.510  0.068  0.279 85.922  0.046  1.937   5.9594e-02
   3_bss:   6.510  0.068  0.279 85.922  0.046  1.937   5.9594e-02
   3_xyz:   7.761  0.061  0.324 80.281  0.057  2.038   1.5014e-01
   3_adp:   7.761  0.061  0.324 80.281  0.057  2.038   1.5014e-01
   3_occ:   7.761  0.061  0.324 80.281  0.057  2.038   1.5014e-01
   4_bss:   7.761  0.061  0.324 80.281  0.057  2.038   1.5014e-01
   4_xyz:   9.028  0.071  0.345 88.868  0.033  2.115   1.6391e-01
   4_adp:   9.028  0.071  0.345 88.868  0.033  2.115   1.6391e-01
   4_occ:   9.028  0.071  0.345 88.868  0.033  2.115   1.6391e-01
   5_bss:   9.028  0.071  0.345 88.868  0.033  2.115   1.6391e-01
   5_xyz:   8.110  0.062  0.273 84.656  0.045  2.270   6.4968e-02
   5_adp:   8.110  0.062  0.273 84.656  0.045  2.270   6.4968e-02
   5_occ:   8.110  0.062  0.273 84.656  0.045  2.270   6.4968e-02
   5_bss:   8.110  0.062  0.273 84.656  0.045  2.270   6.4968e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  88.25   0.00  18.20  88.25   0.00  16.95  88.04   0.00  24.97
   1_occ:  88.25   0.00  18.20  88.25   0.00  16.95  88.04   0.00  24.97
   2_bss:  88.25   0.00  18.20  88.25   0.00  16.95  88.04   0.00  24.97
   2_xyz:  88.25   0.00  18.20  88.25   0.00  16.95  88.04   0.00  24.97
   2_adp:  80.16   0.00  16.31  65.34   0.00  15.02  80.16   0.00  23.35
   2_occ:  80.16   0.00  16.31  65.34   0.00  15.02  80.16   0.00  23.35
   3_bss:  80.16   0.00  16.31  65.34   0.00  15.02  80.16   0.00  23.35
   3_xyz:  80.16   0.00  16.31  65.34   0.00  15.02  80.16   0.00  23.35
   3_adp:  76.88   0.00  16.79  76.88   0.00  14.43  73.65   0.00  29.62
   3_occ:  76.88   0.00  16.79  76.88   0.00  14.43  73.65   0.00  29.62
   4_bss:  76.88   0.00  16.79  76.88   0.00  14.43  73.65   0.00  29.62
   4_xyz:  76.88   0.00  16.79  76.88   0.00  14.43  73.65   0.00  29.62
   4_adp:  88.35   0.00  17.30  88.35   0.00  12.88  85.37   0.00  41.37
   4_occ:  88.35   0.00  17.30  88.35   0.00  12.88  85.37   0.00  41.37
   5_bss:  88.35   0.00  17.30  88.35   0.00  12.88  85.37   0.00  41.37
   5_xyz:  88.35   0.00  17.30  88.35   0.00  12.88  85.37   0.00  41.37
   5_adp:  84.83   0.99  15.92  84.83   0.99  11.58  74.77   3.91  39.56
   5_occ:  84.83   0.99  15.92  84.83   0.99  11.58  74.77   3.91  39.56
   5_bss:  84.87   1.03  15.96  84.87   1.03  11.62  74.81   3.95  39.59
------------------------------------------------------------------------
 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:    1.317    0.015    0.413
   1_adp:    1.317    0.015    0.413
   1_occ:    1.317    0.015    0.413
   2_bss:    1.317    0.015    0.413
   2_xyz:    1.688    0.023    0.551
   2_adp:    1.688    0.023    0.551
   2_occ:    1.688    0.023    0.551
   3_bss:    1.688    0.023    0.551
   3_xyz:    1.742    0.033    0.699
   3_adp:    1.742    0.033    0.699
   3_occ:    1.742    0.033    0.699
   4_bss:    1.742    0.033    0.699
   4_xyz:    2.156    0.055    0.877
   4_adp:    2.156    0.055    0.877
   4_occ:    2.156    0.055    0.877
   5_bss:    2.156    0.055    0.877
   5_xyz:    2.280    0.064    0.951
   5_adp:    2.280    0.064    0.951
   5_occ:    2.280    0.064    0.951
   5_bss:    2.280    0.064    0.951
------------------------------------------------------------------------

CPU time actual refinement: 292.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1217/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 292.27 
  Macro-tasks:
    bulk solvent and scale       = 36.00  
    individual site refinement   = 125.19 
    weights calculation          = 27.42  
    collect and process          = 5.10   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 193.80 
  Micro-tasks:
    mask                            = 2.54   
    f_calc                          = 92.51  
    alpha_beta                      = 7.09   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 100.78 
    fmodel                         = 5.78   
    r_factors                      = 0.26   
    phase_errors                   = 7.78   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 217.90 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.163 micro seconds
Total CPU time: 5.07 minutes
from_scatterers_fft:    611 calls, 92.37 s
gradients_fft:          555 calls, 90.04 s

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

# Date 2008-01-16 Time 03:28:07 PST -0800 (1200482887.73 s)
Start R-work = 0.5204, R-free = 0.5127 (no bulk solvent and anisotropic scale)
Final R-work = 0.1813, R-free = 0.2391 (no bulk solvent and anisotropic scale)

Start R-work = 0.5125, R-free = 0.5028
Final R-work = 0.1668, R-free = 0.2233